|
|
| Line 183: |
Line 183: |
| | | | |
| | Follow the question tree and use the following sample input file as a template | | Follow the question tree and use the following sample input file as a template |
| − |
| |
| − |
| |
| − | Last login: Sat Jan 25 20:39:22 on ttys000
| |
| − | (base) supremestudier@Evans-MBP ~ % ls
| |
| − | 1ay7.cif
| |
| − | 1dqx.cif
| |
| − | 2012-sat-results.csv
| |
| − | 4ees.cif
| |
| − | 5tj3.cif
| |
| − | 6fev.cif
| |
| − | 7rfw.cif
| |
| − | A Hardworking Freshman.txt
| |
| − | A1_Evan.S.ipynb
| |
| − | A2_EvanS.ipynb
| |
| − | AbdulA&YelisvetF_FinalProject_TeenBeachMovieQuiz_.ipynb
| |
| − | An ambitious kid.txt
| |
| − | Applications
| |
| − | Assignment3_EvanS.ipynb
| |
| − | BE.log
| |
| − | Beer's Law.xlsx
| |
| − | Biostats
| |
| − | CYS_waterbox.pdb
| |
| − | Customer Data2.xlsx
| |
| − | Cys.log
| |
| − | Cysteine_waterbox.pdb
| |
| − | Data_EvanS.ipynb
| |
| − | Debugging_EvanS.ipynb
| |
| − | Desktop
| |
| − | Documents
| |
| − | Downloads
| |
| − | Econ160
| |
| − | EvanS_W12.ipynb
| |
| − | Evan_Spector_API_Lab#2.ipynb
| |
| − | Evan_Spector_API_Lab.ipynb
| |
| − | Evan_Spector_API_LabMiniProject.ipynb
| |
| − | Evan_Spector_API_LabMockAPI.ipynb
| |
| − | Evan_Spector_WebScraping_LabDemos.ipynb
| |
| − | Evan_Spector_WebScraping_MiniProject.ipynb
| |
| − | Excel_Evan S.ipynb
| |
| − | Fate.png
| |
| − | Final Exercise.xlsx
| |
| − | Final Project.ipynb
| |
| − | FinalProject_EvanS-2 - Evan H Spector.ipynb
| |
| − | FinalProject_EvanS.ipynb
| |
| − | GS_2.png
| |
| − | G_waterbox.pdb
| |
| − | Gall Diameter by Site Boxplot.png
| |
| − | Game.ipynb
| |
| − | Graph 1 108.xlsx
| |
| − | Graph 2 108.xlsx
| |
| − | Graph 3 108.xlsx
| |
| − | Guest Speaker Walk through.ipynb
| |
| − | Hello World.ipynb
| |
| − | High school Senior Checklist.txt
| |
| − | Invalid Data.xlsx
| |
| − | Keq Data.xlsx
| |
| − | Ksp Data.xlsx
| |
| − | Lab 2_ Evan S..ipynb
| |
| − | Lab3_EvanS.ipynb
| |
| − | Lab5_EvanS.ipynb
| |
| − | Lab_1 Evan S.ipynb
| |
| − | Lat.png
| |
| − | Library
| |
| − | Linear Regression for Dye.xlsx
| |
| − | Loops_EvanS.ipynb
| |
| − | Mambaforge-Darwin-x86_64.
| |
| − | Methyl Red Excel.xlsx
| |
| − | Movies
| |
| − | Music
| |
| − | NBA_players_2015.csv
| |
| − | Overdue Customers 2.xlsx
| |
| − | Oxamide_n2_water.agr
| |
| − | Peer.ipynb
| |
| − | Pictures
| |
| − | Practice.ipynb
| |
| − | Profile Picture.jpg
| |
| − | Project.ipynb
| |
| − | Prototype.ipynb
| |
| − | Prototype_5.ipynb
| |
| − | Public
| |
| − | Quiz Review.ipynb
| |
| − | README.md
| |
| − | Reaction 1 Data.xlsx
| |
| − | Reaction 2 Data.xlsx
| |
| − | Reaction 3 Data.xlsx
| |
| − | Reaction 4 Data.xlsx
| |
| − | Red Cross - Wallet Card - Individual_SD-37055011.pdf
| |
| − | Red Cross Certificate MERGE for Achievement Assignment_SD-37055026.pdf
| |
| − | Review Lab_ Evan S..ipynb
| |
| − | Review3_EvanS.ipynb
| |
| − | Review_2.ipynb
| |
| − | SAT__College_Board__2010_School_Level_Results.csv
| |
| − | Sine and Cosine Curve.ipynb
| |
| − | Split_2.tga
| |
| − | SpotifyFinalProject.ipynb
| |
| − | SulfurCys.agr
| |
| − | TSLA.csv
| |
| − | UNL.agr
| |
| − | Untitled Folder
| |
| − | Untitled.ipynb
| |
| − | Untitled1.ipynb
| |
| − | Untitled2.ipynb
| |
| − | WAT_O.agr
| |
| − | Working with OpenPyXL.xlsx
| |
| − | anaconda3
| |
| − | eclipse
| |
| − | eclipse-workspace
| |
| − | final_project_draft4.ipynb
| |
| − | helloWorld.py
| |
| − | install.sh
| |
| − | introdata.ipynb
| |
| − | java.log.34001
| |
| − | java.log.37118
| |
| − | job_skills.csv
| |
| − | jupyter_mac.command
| |
| − | matlab_crash_dump.6196-1
| |
| − | miniconda3
| |
| − | multiplot.agr
| |
| − | opt
| |
| − | plotting-with-pandas.ipynb
| |
| − | population-by-country-2020.zip
| |
| − | population_by_country_2020.csv
| |
| − | rmsd.agr
| |
| − | source.venv
| |
| − | test.encrypted
| |
| − | test.txt
| |
| − | twitter-workshop-master.zip
| |
| − | (base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Permission denied, please try again.
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Permission denied, please try again.
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − |
| |
| − | (base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login1 ~]$ home
| |
| − | (base) [ehspector@login1 espector]$ cd ..
| |
| − | (base) [ehspector@login1 rizzo]$ cd ..
| |
| − | (base) [ehspector@login1 projects]$ ls
| |
| − | ABCD EssigGroup MaoGroup SchedelGroup
| |
| − | AllamGroup FarhadzadehGroup McDonoughGroup SeeligerGroup
| |
| − | AllenGroup FernandezGroup McGrewGroup SehgalGroup
| |
| − | AMS530 FernandezReuterGroup McKinnonGroup ShepsonGroup
| |
| − | AMS536 FrenkelGroup MehmoodGroup SherGroup
| |
| − | AMS598 FutcherGroup MelikerGroup SheridanGroup
| |
| − | AMS691 GenomicsCore MihalacheGroup ShilkrotGroup
| |
| − | Aponte-RiveraGroup GergenGroup MirandaGroup SiegmannGroup
| |
| − | ArmitageGroup glimm MitchellGroup SladeGroup
| |
| − | AssanisGroup GoblerGroup MoellerGroup SmaersGroup
| |
| − | BEE690 GoldbartGroup MofakhamGroup SOC591
| |
| − | BenchmarkGroup HCPGroup MohantyGroup SOC595
| |
| − | BenderGroup HeinzGroup MollProject StanacevicGroup
| |
| − | BernauerGroup HollisterGroup molssi SternGroup
| |
| − | BialkowskaGroup HoltGroup MoutsanidisGroup SyritsynGroup
| |
| − | BIO303 hpc_support MujicaGroup TakeuchiGroup
| |
| − | BluesteinGroup HudsonGroup NadkarniGroup TanGroup
| |
| − | BurguenoGroup IACSPDPGroup NMRPIJodeyGroup TaylorGroup
| |
| − | CalderGroup JiaoGroup NMRPILipshultzGroup TeraChemGroup
| |
| − | CanliGroup JohnsonGroup NMRPIMingNgaiGroup Tesse
| |
| − | CarlsonGroup JonesBozarthGroup NMRPIPicartGroup TestGroup1
| |
| − | CascanteBonillaGroup JonesGroup OjimaGroup ThackerGroup
| |
| − | ChangGroup JonesSkienaGroup OkeomaGroup ThakurGroup
| |
| − | ChapmanGroup KarzaiGroup PadillaGroup ThorneGroup
| |
| − | CheCastaldoGroup KeeGroup PariseGroup TitleGroup
| |
| − | ChenGroup KeeJiaoGroup PercivalGroup TsybychevGroup
| |
| − | ChenXGroup KellyGroup PerlmanGroup VanSnellenbergGroup
| |
| − | CheungGroup KhosronejadGroup PernaGroup VaskaGroup
| |
| − | ChowdhuryGroup KimGroup PicartGroup VeeramahGroup
| |
| − | ChowdhuryRGroup KirylukGroup PiretGroup VitekGroup
| |
| − | ColleGroup KodnerGroup PolakGroup VonDerLindenGroup
| |
| − | CollierGroup KogaGroup PoonGroup VorkasGroup
| |
| − | CSE416 KozakovGroup PowersGroup WangGroup
| |
| − | CSE504 KritzerGroup PSY610 WanGroup
| |
| − | CSE519 KrsticGroup PSY620 WangXGroup
| |
| − | CSE590 KrsticQuantumGroup QuantComp WeinachtGroup
| |
| − | CSE628 KurcGroup RahmeGroup WeinsteinGroup
| |
| − | DAndreaGroup LeungGroup RajputGroup WeissmanGroup
| |
| − | DavalosGroup LevineGroup RambowGroup WilsonGroup
| |
| − | DeLorenzoGroup LiGroup RestGroup WymoreGroup
| |
| − | DengYasarGroup LoverdeGroup ReuterGroup YeGroup
| |
| − | DevarajanGroup LuGroup RiosGroup YouGroup
| |
| − | DheillyGroup LuhmannGroup rizzo ZhangGroup
| |
| − | DillGroup LuoGroup rjh ZhanGroup
| |
| − | DoboliGroup LynchGroup RosatiGroup ZhangYGroup
| |
| − | DubnauGroup MaffeiGroup samples ZhaoGroup
| |
| − | EBH370 MaGroup SampsonCryoEMGroup ZhouGroup
| |
| − | EBH381 MakGroup SampsonGroup ZhouMedAdvGroup
| |
| − | EkblomGroup MallipattuGroup SamulyakGroup ZhuGroup
| |
| − | (base) [ehspector@login1 projects]$ cd AMS536
| |
| − | (base) [ehspector@login1 AMS536]$ ls
| |
| − | 2017 2019 2021 2023 2025 zzz.anchors
| |
| − | 2018 2020 2022 2024 get_anchors.py zzz.programs
| |
| − | (base) [ehspector@login1 AMS536]$ cd 2025
| |
| − | (base) [ehspector@login1 2025]$ ls
| |
| − | additional_files
| |
| − | (base) [ehspector@login1 2025]$ cd additional_files/
| |
| − | (base) [ehspector@login1 additional_files]$ ls
| |
| − | sample_bashrc_4seawulf.txt sample_slurm_submission.sh touch.sh
| |
| − | (base) [ehspector@login1 additional_files]$ cd ..
| |
| − | (base) [ehspector@login1 2025]$ cd ..
| |
| − | (base) [ehspector@login1 AMS536]$ cd 2025
| |
| − | (base) [ehspector@login1 2025]$ pwd
| |
| − | /gpfs/projects/AMS536/2025
| |
| − | (base) [ehspector@login1 2025]$ vi ~/.bashrc
| |
| − | (base) [ehspector@login1 2025]$ home
| |
| − | (base) [ehspector@login1 espector]$ source ~/.bashrc
| |
| − | (base) [ehspector@login1 espector]$ class
| |
| − | (base) [ehspector@login1 2025]$ home
| |
| − | (base) [ehspector@login1 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login1 espector]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP ~ % ls
| |
| − | 1ay7.cif
| |
| − | 1dqx.cif
| |
| − | 2012-sat-results.csv
| |
| − | 4ees.cif
| |
| − | 5tj3.cif
| |
| − | 6fev.cif
| |
| − | 7rfw.cif
| |
| − | A Hardworking Freshman.txt
| |
| − | A1_Evan.S.ipynb
| |
| − | A2_EvanS.ipynb
| |
| − | AbdulA&YelisvetF_FinalProject_TeenBeachMovieQuiz_.ipynb
| |
| − | An ambitious kid.txt
| |
| − | Applications
| |
| − | Assignment3_EvanS.ipynb
| |
| − | BE.log
| |
| − | Beer's Law.xlsx
| |
| − | Biostats
| |
| − | CYS_waterbox.pdb
| |
| − | Customer Data2.xlsx
| |
| − | Cys.log
| |
| − | Cysteine_waterbox.pdb
| |
| − | Data_EvanS.ipynb
| |
| − | Debugging_EvanS.ipynb
| |
| − | Desktop
| |
| − | Documents
| |
| − | Downloads
| |
| − | Econ160
| |
| − | EvanS_W12.ipynb
| |
| − | Evan_Spector_API_Lab#2.ipynb
| |
| − | Evan_Spector_API_Lab.ipynb
| |
| − | Evan_Spector_API_LabMiniProject.ipynb
| |
| − | Evan_Spector_API_LabMockAPI.ipynb
| |
| − | Evan_Spector_WebScraping_LabDemos.ipynb
| |
| − | Evan_Spector_WebScraping_MiniProject.ipynb
| |
| − | Excel_Evan S.ipynb
| |
| − | Fate.png
| |
| − | Final Exercise.xlsx
| |
| − | Final Project.ipynb
| |
| − | FinalProject_EvanS-2 - Evan H Spector.ipynb
| |
| − | FinalProject_EvanS.ipynb
| |
| − | GS_2.png
| |
| − | G_waterbox.pdb
| |
| − | Gall Diameter by Site Boxplot.png
| |
| − | Game.ipynb
| |
| − | Graph 1 108.xlsx
| |
| − | Graph 2 108.xlsx
| |
| − | Graph 3 108.xlsx
| |
| − | Guest Speaker Walk through.ipynb
| |
| − | Hello World.ipynb
| |
| − | High school Senior Checklist.txt
| |
| − | Invalid Data.xlsx
| |
| − | Keq Data.xlsx
| |
| − | Ksp Data.xlsx
| |
| − | Lab 2_ Evan S..ipynb
| |
| − | Lab3_EvanS.ipynb
| |
| − | Lab5_EvanS.ipynb
| |
| − | Lab_1 Evan S.ipynb
| |
| − | Lat.png
| |
| − | Library
| |
| − | Linear Regression for Dye.xlsx
| |
| − | Loops_EvanS.ipynb
| |
| − | Mambaforge-Darwin-x86_64.
| |
| − | Methyl Red Excel.xlsx
| |
| − | Movies
| |
| − | Music
| |
| − | NBA_players_2015.csv
| |
| − | Overdue Customers 2.xlsx
| |
| − | Oxamide_n2_water.agr
| |
| − | Peer.ipynb
| |
| − | Pictures
| |
| − | Practice.ipynb
| |
| − | Profile Picture.jpg
| |
| − | Project.ipynb
| |
| − | Prototype.ipynb
| |
| − | Prototype_5.ipynb
| |
| − | Public
| |
| − | Quiz Review.ipynb
| |
| − | README.md
| |
| − | Reaction 1 Data.xlsx
| |
| − | Reaction 2 Data.xlsx
| |
| − | Reaction 3 Data.xlsx
| |
| − | Reaction 4 Data.xlsx
| |
| − | Red Cross - Wallet Card - Individual_SD-37055011.pdf
| |
| − | Red Cross Certificate MERGE for Achievement Assignment_SD-37055026.pdf
| |
| − | Review Lab_ Evan S..ipynb
| |
| − | Review3_EvanS.ipynb
| |
| − | Review_2.ipynb
| |
| − | SAT__College_Board__2010_School_Level_Results.csv
| |
| − | Sine and Cosine Curve.ipynb
| |
| − | Split_2.tga
| |
| − | SpotifyFinalProject.ipynb
| |
| − | SulfurCys.agr
| |
| − | TSLA.csv
| |
| − | UNL.agr
| |
| − | Untitled Folder
| |
| − | Untitled.ipynb
| |
| − | Untitled1.ipynb
| |
| − | Untitled2.ipynb
| |
| − | WAT_O.agr
| |
| − | Working with OpenPyXL.xlsx
| |
| − | anaconda3
| |
| − | eclipse
| |
| − | eclipse-workspace
| |
| − | final_project_draft4.ipynb
| |
| − | helloWorld.py
| |
| − | install.sh
| |
| − | introdata.ipynb
| |
| − | java.log.34001
| |
| − | java.log.37118
| |
| − | job_skills.csv
| |
| − | jupyter_mac.command
| |
| − | matlab_crash_dump.6196-1
| |
| − | miniconda3
| |
| − | multiplot.agr
| |
| − | opt
| |
| − | plotting-with-pandas.ipynb
| |
| − | population-by-country-2020.zip
| |
| − | population_by_country_2020.csv
| |
| − | rmsd.agr
| |
| − | source.venv
| |
| − | test.encrypted
| |
| − | test.txt
| |
| − | twitter-workshop-master.zip
| |
| − | (base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login1 ~]$ home
| |
| − | (base) [ehspector@login1 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login1 espector]$ cd 4s0v/
| |
| − | (base) [ehspector@login1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login1 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ cd no_charge/
| |
| − | (base) [ehspector@login1 no_charge]$ ls
| |
| − | 4s0v_no_hydrogens_no_charges.mol2 gas_2.in gas_2.out gas.out_scored.mol2
| |
| − | (base) [ehspector@login1 no_charge]$ cd ..
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi no_gas.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi no_gas.out_scored.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login1 4s0v]$ cd GA_data/
| |
| − | (base) [ehspector@login1 GA_data]$ ls
| |
| − | First_gen_data Last_gen_data
| |
| − | (base) [ehspector@login1 GA_data]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login1 ~]$ home
| |
| − | (base) [ehspector@login1 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login1 espector]$ cd gas_test/
| |
| − | (base) [ehspector@login1 gas_test]$ ls
| |
| − | 4s0v_GA.in 4s0v_GA_output.restart0028.mol2
| |
| − | 4s0v_GA.out 4s0v_GA_output.restart0029.mol2
| |
| − | 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2
| |
| − | 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2
| |
| − | 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2
| |
| − | 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2
| |
| − | 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2
| |
| − | 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2
| |
| − | 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2
| |
| − | 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2
| |
| − | 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2
| |
| − | 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2
| |
| − | 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2
| |
| − | 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2
| |
| − | 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2
| |
| − | 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2
| |
| − | 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2
| |
| − | 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2
| |
| − | 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2
| |
| − | 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2
| |
| − | 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2
| |
| − | 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2
| |
| − | 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2
| |
| − | 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm
| |
| − | 4s0v_GA_output.restart0022.mol2 charge_data
| |
| − | 4s0v_GA_output.restart0023.mol2 gas_f_test
| |
| − | 4s0v_GA_output.restart0024.mol2 gas_RD_Test
| |
| − | 4s0v_GA_output.restart0025.mol2 GA.txt
| |
| − | 4s0v_GA_output.restart0026.mol2 test_2.in
| |
| − | 4s0v_GA_output.restart0027.mol2 test.in
| |
| − | (base) [ehspector@login1 gas_test]$ cd ..
| |
| − | (base) [ehspector@login1 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login1 espector]$ cd 4s0v/
| |
| − | (base) [ehspector@login1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login1 4s0v]$ cd s
| |
| − | -bash: cd: s: No such file or directory
| |
| − | (base) [ehspector@login1 4s0v]$ cd structure/
| |
| − | (base) [ehspector@login1 structure]$ ls
| |
| − | 4s0v_ligand_hydrogens_charges.mol2 4s0v_no_hydrogens_no_charges.mol2
| |
| − | 4s0v_ligand_no_hydrogens_no_charges.mol2 4s0v_protein_with_charges.mol2
| |
| − | (base) [ehspector@login1 structure]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login1 4s0v]$ cd ..
| |
| − | (base) [ehspector@login1 espector]$ cd gas_test/
| |
| − | (base) [ehspector@login1 gas_test]$ ls
| |
| − | 4s0v_GA.in 4s0v_GA_output.restart0028.mol2
| |
| − | 4s0v_GA.out 4s0v_GA_output.restart0029.mol2
| |
| − | 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2
| |
| − | 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2
| |
| − | 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2
| |
| − | 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2
| |
| − | 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2
| |
| − | 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2
| |
| − | 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2
| |
| − | 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2
| |
| − | 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2
| |
| − | 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2
| |
| − | 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2
| |
| − | 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2
| |
| − | 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2
| |
| − | 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2
| |
| − | 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2
| |
| − | 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2
| |
| − | 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2
| |
| − | 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2
| |
| − | 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2
| |
| − | 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2
| |
| − | 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2
| |
| − | 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm
| |
| − | 4s0v_GA_output.restart0022.mol2 charge_data
| |
| − | 4s0v_GA_output.restart0023.mol2 gas_f_test
| |
| − | 4s0v_GA_output.restart0024.mol2 gas_RD_Test
| |
| − | 4s0v_GA_output.restart0025.mol2 GA.txt
| |
| − | 4s0v_GA_output.restart0026.mol2 test_2.in
| |
| − | 4s0v_GA_output.restart0027.mol2 test.in
| |
| − | (base) [ehspector@login1 gas_test]$ cd gas_f_test/
| |
| − | (base) [ehspector@login1 gas_f_test]$ ls
| |
| − | diff.out gas_0.out_scored.mol2 gas_1.out gas_50.in gas_50.out_scored.mol2
| |
| − | gas_0.out gas_1.in gas_1.out_scored.mol2 gas_50.out
| |
| − | (base) [ehspector@login1 gas_f_test]$ vi gas_1.in
| |
| − | (base) [ehspector@login1 gas_f_test]$ cd ..
| |
| − | (base) [ehspector@login1 gas_test]$ ls
| |
| − | 4s0v_GA.in 4s0v_GA_output.restart0028.mol2
| |
| − | 4s0v_GA.out 4s0v_GA_output.restart0029.mol2
| |
| − | 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2
| |
| − | 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2
| |
| − | 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2
| |
| − | 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2
| |
| − | 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2
| |
| − | 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2
| |
| − | 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2
| |
| − | 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2
| |
| − | 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2
| |
| − | 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2
| |
| − | 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2
| |
| − | 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2
| |
| − | 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2
| |
| − | 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2
| |
| − | 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2
| |
| − | 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2
| |
| − | 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2
| |
| − | 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2
| |
| − | 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2
| |
| − | 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2
| |
| − | 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2
| |
| − | 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm
| |
| − | 4s0v_GA_output.restart0022.mol2 charge_data
| |
| − | 4s0v_GA_output.restart0023.mol2 gas_f_test
| |
| − | 4s0v_GA_output.restart0024.mol2 gas_RD_Test
| |
| − | 4s0v_GA_output.restart0025.mol2 GA.txt
| |
| − | 4s0v_GA_output.restart0026.mol2 test_2.in
| |
| − | 4s0v_GA_output.restart0027.mol2 test.in
| |
| − | (base) [ehspector@login1 gas_test]$ cd ..
| |
| − | (base) [ehspector@login1 espector]$ cd 4s0v/gas_teiger/
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ module
| |
| − | Modules Release 4.0.0 (2017-10-16)
| |
| − | Usage: module [options] [command] [args ...]
| |
| − |
| |
| − | Loading / Unloading commands:
| |
| − | add | load modulefile [...] Load modulefile(s)
| |
| − | rm | unload modulefile [...] Remove modulefile(s)
| |
| − | purge Unload all loaded modulefiles
| |
| − | reload | refresh Unload then load all loaded modulefiles
| |
| − | switch | swap [mod1] mod2 Unload mod1 and load mod2
| |
| − |
| |
| − | Listing / Searching commands:
| |
| − | list [-t|-l] List loaded modules
| |
| − | avail [-d|-L] [-t|-l] [mod ...] List all or matching available modules
| |
| − | aliases List all module aliases
| |
| − | whatis [modulefile ...] Print whatis information of modulefile(s)
| |
| − | apropos | keyword | search str Search all name and whatis containing str
| |
| − |
| |
| − | Collection of modules handling commands:
| |
| − | save [collection|file] Save current module list to collection
| |
| − | restore [collection|file] Restore module list from collection or file
| |
| − | saverm [collection] Remove saved collection
| |
| − | saveshow [collection|file] Display information about collection
| |
| − | savelist [-t|-l] List all saved collections
| |
| − |
| |
| − | Shell's initialization files handling commands:
| |
| − | initlist List all modules loaded from init file
| |
| − | initadd modulefile [...] Add modulefile to shell init file
| |
| − | initrm modulefile [...] Remove modulefile from shell init file
| |
| − | initprepend modulefile [...] Add to beginning of list in init file
| |
| − | initswitch mod1 mod2 Switch mod1 with mod2 from init file
| |
| − | initclear Clear all modulefiles from init file
| |
| − |
| |
| − | Other commands:
| |
| − | help [modulefile ...] Print this or modulefile(s) help info
| |
| − | display | show modulefile [...] Display information about modulefile(s)
| |
| − | test [modulefile ...] Test modulefile(s)
| |
| − | use [-a|-p] dir [...] Add dir(s) to MODULEPATH variable
| |
| − | unuse dir [...] Remove dir(s) from MODULEPATH variable
| |
| − | path modulefile Print modulefile path
| |
| − | paths modulefile Print path of matching available modules
| |
| − | source scriptfile [...] Execute scriptfile(s)
| |
| − |
| |
| − | Switches:
| |
| − | -t | --terse Display output in terse format
| |
| − | -l | --long Display output in long format
| |
| − | -d | --default Only show default versions available
| |
| − | -L | --latest Only show latest versions available
| |
| − | -a | --append Append directory to MODULEPATH
| |
| − | -p | --prepend Prepend directory to MODULEPATH
| |
| − |
| |
| − | Options:
| |
| − | -h | --help This usage info
| |
| − | -V | --version Module version
| |
| − | -D | --debug Enable debug messages
| |
| − | (base) [ehspector@login1 gas_teiger]$ module list
| |
| − | Currently Loaded Modulefiles:
| |
| − | 1) slurm/17.11.12 2) shared
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login1 4s0v]$ cd structure/
| |
| − | (base) [ehspector@login1 structure]$ ls
| |
| − | 4s0v_ligand_hydrogens_charges.mol2 4s0v_no_hydrogens_no_charges.mol2
| |
| − | 4s0v_ligand_no_hydrogens_no_charges.mol2 4s0v_protein_with_charges.mol2
| |
| − | (base) [ehspector@login1 structure]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login1 4s0v]$ vi gas_teiger/
| |
| − | (base) [ehspector@login1 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login1 4s0v]$ cd energy_min/
| |
| − | (base) [ehspector@login1 energy_min]$ ls
| |
| − | 4s0v.lig.min_scored.mol2 min.in min.out
| |
| − | (base) [ehspector@login1 energy_min]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ cd ..
| |
| − | (base) [ehspector@login1 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login1 espector]$ cd 4s0v/
| |
| − | (base) [ehspector@login1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login1 4s0v]$ vi gas_teiger/
| |
| − | (base) [ehspector@login1 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ cd surface_spheres/
| |
| − | (base) [ehspector@login1 surface_spheres]$ ls
| |
| − | 4s0v_binding_spheres.sph 4s0v_surface.dms INSPH OUTSPH selected_spheres.sph
| |
| − | (base) [ehspector@login1 surface_spheres]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ cd ..
| |
| − | (base) [ehspector@login1 espector]$ cd gas_test/
| |
| − | (base) [ehspector@login1 gas_test]$ ls
| |
| − | 4s0v_GA.in 4s0v_GA_output.restart0028.mol2
| |
| − | 4s0v_GA.out 4s0v_GA_output.restart0029.mol2
| |
| − | 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2
| |
| − | 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2
| |
| − | 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2
| |
| − | 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2
| |
| − | 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2
| |
| − | 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2
| |
| − | 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2
| |
| − | 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2
| |
| − | 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2
| |
| − | 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2
| |
| − | 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2
| |
| − | 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2
| |
| − | 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2
| |
| − | 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2
| |
| − | 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2
| |
| − | 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2
| |
| − | 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2
| |
| − | 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2
| |
| − | 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2
| |
| − | 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2
| |
| − | 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2
| |
| − | 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm
| |
| − | 4s0v_GA_output.restart0022.mol2 charge_data
| |
| − | 4s0v_GA_output.restart0023.mol2 gas_f_test
| |
| − | 4s0v_GA_output.restart0024.mol2 gas_RD_Test
| |
| − | 4s0v_GA_output.restart0025.mol2 GA.txt
| |
| − | 4s0v_GA_output.restart0026.mol2 test_2.in
| |
| − | 4s0v_GA_output.restart0027.mol2 test.in
| |
| − | (base) [ehspector@login1 gas_test]$ cd ..
| |
| − | (base) [ehspector@login1 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login1 espector]$ cd 4s0v/
| |
| − | (base) [ehspector@login1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login1 4s0v]$ cd surface_spheres/
| |
| − | (base) [ehspector@login1 surface_spheres]$ ls
| |
| − | 4s0v_binding_spheres.sph 4s0v_surface.dms INSPH OUTSPH selected_spheres.sph
| |
| − | (base) [ehspector@login1 surface_spheres]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login1 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ dock6 -i gas.in -o gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas.out_scored.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login2 ~]$ home
| |
| − | (base) [ehspector@login2 espector]$ class
| |
| − | (base) [ehspector@login2 2025]$ ls
| |
| − | additional_files
| |
| − | (base) [ehspector@login2 2025]$ cd additional_files/
| |
| − | (base) [ehspector@login2 additional_files]$ ls
| |
| − | sample_bashrc_4seawulf.txt sample_slurm_submission.sh touch.sh
| |
| − | (base) [ehspector@login2 additional_files]$ vi sample_bashrc_4seawulf.txt
| |
| − | (base) [ehspector@login2 additional_files]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP ~ % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login2 ~]$ home
| |
| − | (base) [ehspector@login2 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login2 espector]$ cd builds/
| |
| − | (base) [ehspector@login2 builds]$ cd alpha_branch/
| |
| − | (base) [ehspector@login2 alpha_branch]$ ls
| |
| − | bin docs parameters README.md template_pipeline
| |
| − | developer install README src tutorials
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@login2 install]$ ls
| |
| − | bluegenel gnu.acml homebrew intel.mkl sgi
| |
| − | bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel
| |
| − | config.h gnu.parallel ibmaix Makefile test
| |
| − | configure gnu.parallel.rdkit intel oneapi
| |
| − | docker gnu.rdkit intel.intelmpi.parallel pgi
| |
| − | gnu gnu.valgrind intel.ip.mkl rules.h
| |
| − | (base) [ehspector@login2 install]$ cd ..
| |
| − | (base) [ehspector@login2 alpha_branch]$ l
| |
| − | bash: l: command not found...
| |
| − | (base) [ehspector@login2 alpha_branch]$ ls
| |
| − | bin docs parameters README.md template_pipeline
| |
| − | developer install README src tutorials
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@login2 install]$ ls
| |
| − | bluegenel gnu.acml homebrew intel.mkl sgi
| |
| − | bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel
| |
| − | config.h gnu.parallel ibmaix Makefile test
| |
| − | configure gnu.parallel.rdkit intel oneapi
| |
| − | docker gnu.rdkit intel.intelmpi.parallel pgi
| |
| − | gnu gnu.valgrind intel.ip.mkl rules.h
| |
| − | (base) [ehspector@login2 install]$ cd ..
| |
| − | (base) [ehspector@login2 alpha_branch]$ ls
| |
| − | bin docs parameters README.md template_pipeline
| |
| − | developer install README src tutorials
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd bin/
| |
| − | (base) [ehspector@login2 bin]$ ls
| |
| − | dock6 dock6.rdkit
| |
| − | (base) [ehspector@login2 bin]$ vi dock6.rdkit
| |
| − | (base) [ehspector@login2 bin]$ cd ..
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd src/
| |
| − | (base) [ehspector@login2 src]$ ls
| |
| − | accessories dock gbsa_grids Makefile rdkit tleap
| |
| − | antechamber docktools grid mopac6 resp
| |
| − | (base) [ehspector@login2 src]$ vi Makefile
| |
| − | (base) [ehspector@login2 src]$ cd rdkit/
| |
| − | (base) [ehspector@login2 rdkit]$ ls
| |
| − | boost boost_1_71_0.tar.gz eigen-3.3.9.tar.gz rdkit-Release_2019_09_1
| |
| − | boost_1_71_0 eigen-3.3.9 Makefile rdkit-Release_2019_09_1.tar.gz
| |
| − | (base) [ehspector@login2 rdkit]$ vi Makefile
| |
| − | (base) [ehspector@login2 rdkit]$ vi Makefile
| |
| − | (base) [ehspector@login2 rdkit]$ vi Makefile
| |
| − | (base) [ehspector@login2 rdkit]$ ls
| |
| − | boost boost_1_71_0.tar.gz eigen-3.3.9.tar.gz rdkit-Release_2019_09_1
| |
| − | boost_1_71_0 eigen-3.3.9 Makefile rdkit-Release_2019_09_1.tar.gz
| |
| − | (base) [ehspector@login2 rdkit]$ module list
| |
| − | Currently Loaded Modulefiles:
| |
| − | 1) slurm/17.11.12 2) shared
| |
| − | (base) [ehspector@login2 rdkit]$ module load git
| |
| − | WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.
| |
| − | /cm/local/apps/environment-modules/4.0.0//bin
| |
| − | (base) [ehspector@login2 rdkit]$ module list
| |
| − | Currently Loaded Modulefiles:
| |
| − | 1) slurm/17.11.12 2) shared 3) git/2.36.2
| |
| − | (base) [ehspector@login2 rdkit]$ git branch
| |
| − | * alpha_branch
| |
| − | master
| |
| − | (base) [ehspector@login2 rdkit]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP ~ % cd Desktop/GradSchool/StonyBrook/Semester/Spring_25
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ls
| |
| − | AMS_500 AMS_537 AMS_691
| |
| − | AMS_536 AMS_548 CARS_551
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % cd AMS_691
| |
| − | (base) supremestudier@Evans-MBP AMS_691 % ls
| |
| − | AMS691_01.pdf Projects Text_book
| |
| − | (base) supremestudier@Evans-MBP AMS_691 % mkdir Lectures
| |
| − | (base) supremestudier@Evans-MBP AMS_691 % cd ..
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % cd AMS_500
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % ls
| |
| − | 2010.06.08_hadjiargyrou.pdf
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % mkdir Materials
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % mv 2010.06.08_hadjiargyrou.pdf Materials
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % ls
| |
| − | Materials
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % cd ..
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % cd CARS_551
| |
| − | (base) supremestudier@Evans-MBP CARS_551 % ls
| |
| − | (base) supremestudier@Evans-MBP CARS_551 % cd ..
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login2 ~]$ home
| |
| − | (base) [ehspector@login2 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login2 espector]$ cd gas_test/
| |
| − | (base) [ehspector@login2 gas_test]$ ls
| |
| − | 4s0v_GA.in 4s0v_GA_output.restart0028.mol2
| |
| − | 4s0v_GA.out 4s0v_GA_output.restart0029.mol2
| |
| − | 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2
| |
| − | 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2
| |
| − | 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2
| |
| − | 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2
| |
| − | 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2
| |
| − | 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2
| |
| − | 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2
| |
| − | 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2
| |
| − | 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2
| |
| − | 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2
| |
| − | 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2
| |
| − | 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2
| |
| − | 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2
| |
| − | 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2
| |
| − | 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2
| |
| − | 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2
| |
| − | 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2
| |
| − | 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2
| |
| − | 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2
| |
| − | 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2
| |
| − | 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2
| |
| − | 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm
| |
| − | 4s0v_GA_output.restart0022.mol2 charge_data
| |
| − | 4s0v_GA_output.restart0023.mol2 gas_f_test
| |
| − | 4s0v_GA_output.restart0024.mol2 gas_RD_Test
| |
| − | 4s0v_GA_output.restart0025.mol2 GA.txt
| |
| − | 4s0v_GA_output.restart0026.mol2 test_2.in
| |
| − | 4s0v_GA_output.restart0027.mol2 test.in
| |
| − | (base) [ehspector@login2 gas_test]$ cd ..
| |
| − | (base) [ehspector@login2 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login2 espector]$ cd 4s0v/
| |
| − | (base) [ehspector@login2 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login2 4s0v]$ cd structure/
| |
| − | (base) [ehspector@login2 structure]$ ls
| |
| − | 4s0v_ligand_hydrogens_charges.mol2 4s0v_no_hydrogens_no_charges.mol2
| |
| − | 4s0v_ligand_no_hydrogens_no_charges.mol2 4s0v_protein_with_charges.mol2
| |
| − | (base) [ehspector@login2 structure]$ cd ..
| |
| − | (base) [ehspector@login2 4s0v]$ cp structure/4s0v_ligand_hydrogens_charges.mol2 gas_teiger/
| |
| − | (base) [ehspector@login2 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@login2 gas_teiger]$ ls
| |
| − | 4s0v_ligand_hydrogens_charges.mol2 gas.out no_charge no_gas.out
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi 4s0v_ligand_hydrogens_charges.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi 4s0v_ligand_hydrogens_charges.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ pwd
| |
| − | /gpfs/projects/rizzo/espector/4s0v/gas_teiger
| |
| − | (base) [ehspector@login2 gas_teiger]$ ls
| |
| − | 4s0v_ligand_hydrogens_charges.mol2 gas.out no_charge no_gas.out
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ cd no_charge/
| |
| − | (base) [ehspector@login2 no_charge]$ ls
| |
| − | 4s0v_no_hydrogens_no_charges.mol2 gas_2.in gas_2.out gas.out_scored.mol2
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.in
| |
| − | (base) [ehspector@login2 no_charge]$ cd ..
| |
| − | (base) [ehspector@login2 gas_teiger]$ mv 4s0v_ligand_hydrogens_charges.mol2 no_charge/
| |
| − | (base) [ehspector@login2 gas_teiger]$ cd no_charge/
| |
| − | (base) [ehspector@login2 no_charge]$ ls
| |
| − | 4s0v_ligand_hydrogens_charges.mol2 gas_2.in gas.out_scored.mol2
| |
| − | 4s0v_no_hydrogens_no_charges.mol2 gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.in
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.in
| |
| − | (base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.in
| |
| − | (base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ ls
| |
| − | 4s0v_ligand_hydrogens_charges.mol2 gas_2.in gas.out_scored.mol2
| |
| − | 4s0v_no_hydrogens_no_charges.mol2 gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.in
| |
| − | (base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ ls
| |
| − | 4s0v_ligand_hydrogens_charges.mol2 gas_2.in gas.out_scored.mol2
| |
| − | 4s0v_no_hydrogens_no_charges.mol2 gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ mv 4s0v_ligand_hydrogens_charges.mol2 4s0v_ligand_hydrogens_no_charges.mol2
| |
| − | (base) [ehspector@login2 no_charge]$ ls
| |
| − | 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in gas.out_scored.mol2
| |
| − | 4s0v_no_hydrogens_no_charges.mol2 gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ cd ..
| |
| − | (base) [ehspector@login2 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@login2 4s0v]$ cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/no_charge/
| |
| − | (base) [ehspector@login2 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login2 4s0v]$ cd gas_teiger/no_charge/
| |
| − | (base) [ehspector@login2 no_charge]$ ls
| |
| − | 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in
| |
| − | 4s0v.lig.min_scored.mol2 gas_2.out
| |
| − | 4s0v_no_hydrogens_no_charges.mol2 gas.out_scored.mol2
| |
| − | (base) [ehspector@login2 no_charge]$ vi 4s0v.lig.min_scored.mol2
| |
| − | (base) [ehspector@login2 no_charge]$ vimdiff 4s0v.lig.min_scored.mol2 4s0v_ligand_hydrogens_no_charges.mol2
| |
| − | 2 files to edit
| |
| − | (base) [ehspector@login2 no_charge]$ vi 4s0v.lig.min_scored.mol2
| |
| − | (base) [ehspector@login2 no_charge]$ mv 4s0v.lig.min_scored.mol2 4s0v.lig_no_charge.min_scored.mol2
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.in
| |
| − | (base) [ehspector@login2 no_charge]$ dock6 -i gas_2.in -o gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ ls
| |
| − | 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in
| |
| − | 4s0v.lig_no_charge.min_scored.mol2 gas_2.out
| |
| − | 4s0v_no_hydrogens_no_charges.mol2 gas.out_scored.mol2
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.in
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas.out_scored.mol2
| |
| − | (base) [ehspector@login2 no_charge]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login2 ~]$ home
| |
| − | (base) [ehspector@login2 espector]$ cd 4s0v/
| |
| − | (base) [ehspector@login2 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login2 4s0v]$ cd gas_teiger/no_charge/
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.in
| |
| − | (base) [ehspector@login2 no_charge]$ vi 4s0v.lig_no_charge.min_scored.mol2
| |
| − | (base) [ehspector@login2 no_charge]$ vi gas_2.out
| |
| − | (base) [ehspector@login2 no_charge]$ cd ..
| |
| − | (base) [ehspector@login2 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas.in
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login2 ~]$ home
| |
| − | (base) [ehspector@login2 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login2 espector]$ cd 4s0v/
| |
| − | (base) [ehspector@login2 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@login2 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@login2 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi no_gas.in
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi no_gas.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi no_gas.out_scored.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login1 ~]$ class
| |
| − | (base) [ehspector@login1 2025]$ pwd
| |
| − | /gpfs/projects/AMS536/2025
| |
| − | (base) [ehspector@login1 2025]$ cd ..
| |
| − | (base) [ehspector@login1 AMS536]$ vi ~/.bashrc
| |
| − | (base) [ehspector@login1 AMS536]$ source ~/.bashrc
| |
| − | WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.
| |
| − | /cm/local/apps/environment-modules/4.0.0//bin
| |
| − | (base) [ehspector@login1 AMS536]$ home
| |
| − | (base) [ehspector@login1 espector]$ class
| |
| − | (base) [ehspector@login1 2025]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % tutor
| |
| − | zsh: command not found: tutor
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % vimtutor
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login2 ~]$ class
| |
| − | (base) [ehspector@login2 2025]$ mkdir ehspector
| |
| − | mkdir: cannot create directory ‘ehspector’: Permission denied
| |
| − | (base) [ehspector@login2 2025]$ mkdir ehspector
| |
| − | (base) [ehspector@login2 2025]$ ls
| |
| − | additional_files ehspector ooreilly
| |
| − | (base) [ehspector@login2 2025]$ cd ehspector/
| |
| − | (base) [ehspector@login2 ehspector]$ ls
| |
| − | (base) [ehspector@login2 ehspector]$ touch file.txt
| |
| − | (base) [ehspector@login2 ehspector]$ ls
| |
| − | (base) [ehspector@login2 ehspector]$ cd ..
| |
| − | (base) [ehspector@login2 2025]$ cd ..
| |
| − | (base) [ehspector@login2 AMS536]$ cd
| |
| − | (base) [ehspector@login2 ~]$ ls
| |
| − | miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@login2 ~]$ mkdir class_project
| |
| − | (base) [ehspector@login2 ~]$ ls
| |
| − | class_project miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@login2 ~]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ssh: connect to host login.seawulf.stonybrook.edu port 22: Undefined error: 0
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login1 ~]$ home
| |
| − | (base) [ehspector@login1 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login1 espector]$ cd builds/
| |
| − | (base) [ehspector@login1 builds]$ ls
| |
| − | alpha_branch dock6-master dock6-master.zip dock6-rdkit
| |
| − | (base) [ehspector@login1 builds]$ cd alpha_branch/
| |
| − | (base) [ehspector@login1 alpha_branch]$ ls
| |
| − | bin docs parameters README.md template_pipeline
| |
| − | developer install README src tutorials
| |
| − | (base) [ehspector@login1 alpha_branch]$ module load git
| |
| − | WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.
| |
| − | /cm/local/apps/environment-modules/4.0.0//bin
| |
| − | (base) [ehspector@login1 alpha_branch]$ git branch
| |
| − | * alpha_branch
| |
| − | master
| |
| − | (base) [ehspector@login1 alpha_branch]$ git config --get remote.origin.url
| |
| − | https://github.com/EvanS-Dock6/dock6.git
| |
| − | (base) [ehspector@login1 alpha_branch]$ git pull
| |
| − | Username for 'https://github.com': EvanS_Dock6
| |
| − | Password for 'https://EvanS_Dock6@github.com':
| |
| − | remote: Support for password authentication was removed on August 13, 2021.
| |
| − | remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication.
| |
| − | fatal: Authentication failed for 'https://github.com/EvanS-Dock6/dock6.git/'
| |
| − | (base) [ehspector@login1 alpha_branch]$ git pull
| |
| − | Username for 'https://github.com': EvanS-Dock6
| |
| − | Password for 'https://EvanS-Dock6@github.com':
| |
| − | remote: Support for password authentication was removed on August 13, 2021.
| |
| − | remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication.
| |
| − | fatal: Authentication failed for 'https://github.com/EvanS-Dock6/dock6.git/'
| |
| − | (base) [ehspector@login1 alpha_branch]$ git pull
| |
| − | Username for 'https://github.com': EvanS-Dock6
| |
| − | Password for 'https://EvanS-Dock6@github.com':
| |
| − | remote: Enumerating objects: 1129, done.
| |
| − | remote: Counting objects: 100% (672/672), done.
| |
| − | remote: Compressing objects: 100% (147/147), done.
| |
| − | remote: Total 1129 (delta 585), reused 561 (delta 525), pack-reused 457 (from 1)
| |
| − | Receiving objects: 100% (1129/1129), 1.09 MiB | 13.11 MiB/s, done.
| |
| − | Resolving deltas: 100% (909/909), completed with 45 local objects.
| |
| − | From https://github.com/EvanS-Dock6/dock6
| |
| − | 4be5c842..2ce698b4 alpha_branch -> origin/alpha_branch
| |
| − | 50ce88e6..da80bfc9 master -> origin/master
| |
| − | Updating 4be5c842..2ce698b4
| |
| − | error: Your local changes to the following files would be overwritten by merge:
| |
| − | src/dock/dock.cpp
| |
| − | src/dock/orient.cpp
| |
| − | src/dock/sphere.cpp
| |
| − | Please commit your changes or stash them before you merge.
| |
| − | Aborting
| |
| − | (base) [ehspector@login1 alpha_branch]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
| |
| − | (use "git pull" to update your local branch)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add/rm <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | deleted: install/test/minimization/minimize7.dockout
| |
| − | modified: src/dock/dock.cpp
| |
| − | modified: src/dock/filter.cpp
| |
| − | modified: src/dock/filter.h
| |
| − | modified: src/dock/gasteiger.cpp
| |
| − | modified: src/dock/orient.cpp
| |
| − | modified: src/dock/sphere.cpp
| |
| − | modified: src/rdkit/Makefile
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | src/dock/lol
| |
| − | src/rdkit/boost/
| |
| − | src/rdkit/boost_1_71_0.tar.gz
| |
| − | src/rdkit/boost_1_71_0/
| |
| − | src/rdkit/eigen-3.3.9.tar.gz
| |
| − | src/rdkit/eigen-3.3.9/
| |
| − | src/rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | src/rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@login1 alpha_branch]$ git diff src/dock/dock.cpp
| |
| − | diff --git a/src/dock/dock.cpp b/src/dock/dock.cpp
| |
| − | index 81925eac..e447b601 100644
| |
| − | --- a/src/dock/dock.cpp
| |
| − | +++ b/src/dock/dock.cpp
| |
| − | @@ -820,7 +820,7 @@ main(int argc, char **argv)
| |
| − | if (c_filter.use_database_filter)
| |
| − | {
| |
| − | //calculate RDKIT-related descriptors for the ligand
| |
| − | - c_filter.calc_descriptors(mol);
| |
| − | + c_filter.calc_descriptors(mol, c_typer);
| |
| − | //other descriptors are now computed & printed in amber_typer.cpp
| |
| − | //print out the descriptors
| |
| − | //cout << c_filter.get_descriptors(mol);
| |
| − | (base) [ehspector@login1 alpha_branch]$ git diff src/dock/gasteiger.cpp
| |
| − | diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp
| |
| − | index 5cfba835..3a967b89 100644
| |
| − | --- a/src/dock/gasteiger.cpp
| |
| − | +++ b/src/dock/gasteiger.cpp
| |
| − | @@ -272,7 +272,7 @@ compute_gast_charges(DOCKMol & mol) {
| |
| − |
| |
| − | //Fochmod
| |
| − | //printf("gasteiger mark #1 \n");
| |
| − | -
| |
| − | + cout << "The for loop is initiated" << endl;
| |
| − | for (int a = 0; a < mol.num_atoms; a++) {
| |
| − | //printf("switchloop %d \n", a);
| |
| − | switch (mol.atom_envs[a][1]) {
| |
| − | @@ -283,6 +283,7 @@ compute_gast_charges(DOCKMol & mol) {
| |
| − | param_b[a] = 9.18;
| |
| − | param_c[a] = 1.88;
| |
| − | param_d[a] = param_a[a] + param_b[a] + param_c[a];
| |
| − | + cout << "This is the charge" << endl;
| |
| − | break;
| |
| − | case 'B': //C.2 trtrtr pi
| |
| − | tot_charges[a] = 0.0;
| |
| − | (base) [ehspector@login1 alpha_branch]$ git diff src/dock/orient.cpp
| |
| − | diff --git a/src/dock/orient.cpp b/src/dock/orient.cpp
| |
| − | index 92d58f71..2d63fece 100644
| |
| − | --- a/src/dock/orient.cpp
| |
| − | +++ b/src/dock/orient.cpp
| |
| − | @@ -461,8 +461,7 @@ Orient::get_spheres()
| |
| − | spheres = Active_Site_Spheres :: get_instance();
| |
| − | num_spheres = spheres.size();
| |
| − |
| |
| − | - if (verbose) cout << "Read in " << num_spheres
| |
| − | - << " spheres for orienting." << endl;
| |
| − | + cout << "Read in " << num_spheres << " spheres for orienting." << endl;
| |
| − |
| |
| − | // process critical points
| |
| − | if (critical_points) {
| |
| − | (base) [ehspector@login1 alpha_branch]$ git diff src/dock/sphere.cpp
| |
| − | diff --git a/src/dock/sphere.cpp b/src/dock/sphere.cpp
| |
| − | index 27641d83..5739a67c 100644
| |
| − | --- a/src/dock/sphere.cpp
| |
| − | +++ b/src/dock/sphere.cpp
| |
| − | @@ -111,6 +111,7 @@ read_spheres( string sphere_file_name, SphereVec & spheres )
| |
| − | fclose(sphere_file);
| |
| − |
| |
| − | return num_spheres;
| |
| − | +
| |
| − | }
| |
| − |
| |
| − |
| |
| − | (base) [ehspector@login1 alpha_branch]$ ls
| |
| − | bin docs parameters README.md template_pipeline
| |
| − | developer install README src tutorials
| |
| − | (base) [ehspector@login1 alpha_branch]$ cd src/dock
| |
| − | (base) [ehspector@login1 dock]$ vi gasteiger.cpp
| |
| − | (base) [ehspector@login1 dock]$ git diff gasteiger.cpp
| |
| − | diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp
| |
| − | index 5cfba835..3a967b89 100644
| |
| − | --- a/src/dock/gasteiger.cpp
| |
| − | +++ b/src/dock/gasteiger.cpp
| |
| − | @@ -272,7 +272,7 @@ compute_gast_charges(DOCKMol & mol) {
| |
| − |
| |
| − | //Fochmod
| |
| − | //printf("gasteiger mark #1 \n");
| |
| − | -
| |
| − | + cout << "The for loop is initiated" << endl;
| |
| − | for (int a = 0; a < mol.num_atoms; a++) {
| |
| − | //printf("switchloop %d \n", a);
| |
| − | switch (mol.atom_envs[a][1]) {
| |
| − | @@ -283,6 +283,7 @@ compute_gast_charges(DOCKMol & mol) {
| |
| − | param_b[a] = 9.18;
| |
| − | param_c[a] = 1.88;
| |
| − | param_d[a] = param_a[a] + param_b[a] + param_c[a];
| |
| − | + cout << "This is the charge" << endl;
| |
| − | break;
| |
| − | case 'B': //C.2 trtrtr pi
| |
| − | tot_charges[a] = 0.0;
| |
| − | (base) [ehspector@login1 dock]$ vi gasteiger.cpp
| |
| − | (base) [ehspector@login1 dock]$ git diff gasteiger.cpp
| |
| − | diff --git a/src/dock/gasteiger.cpp b/src/dock/gasteiger.cpp
| |
| − | index 5cfba835..e82d5397 100644
| |
| − | --- a/src/dock/gasteiger.cpp
| |
| − | +++ b/src/dock/gasteiger.cpp
| |
| − | @@ -272,7 +272,6 @@ compute_gast_charges(DOCKMol & mol) {
| |
| − |
| |
| − | //Fochmod
| |
| − | //printf("gasteiger mark #1 \n");
| |
| − | -
| |
| − | for (int a = 0; a < mol.num_atoms; a++) {
| |
| − | //printf("switchloop %d \n", a);
| |
| − | switch (mol.atom_envs[a][1]) {
| |
| − | (base) [ehspector@login1 dock]$ git status gasteiger.cpp
| |
| − | On branch alpha_branch
| |
| − | Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
| |
| − | (use "git pull" to update your local branch)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | modified: gasteiger.cpp
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@login1 dock]$ vi gasteiger.cpp
| |
| − | (base) [ehspector@login1 dock]$ git diff gasteiger.cpp
| |
| − | (base) [ehspector@login1 dock]$ git status gasteiger.cpp
| |
| − | On branch alpha_branch
| |
| − | Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
| |
| − | (use "git pull" to update your local branch)
| |
| − |
| |
| − | nothing to commit, working tree clean
| |
| − | (base) [ehspector@login1 dock]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
| |
| − | (use "git pull" to update your local branch)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add/rm <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | deleted: ../../install/test/minimization/minimize7.dockout
| |
| − | modified: dock.cpp
| |
| − | modified: filter.cpp
| |
| − | modified: filter.h
| |
| − | modified: orient.cpp
| |
| − | modified: sphere.cpp
| |
| − | modified: ../rdkit/Makefile
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | lol
| |
| − | ../rdkit/boost/
| |
| − | ../rdkit/boost_1_71_0.tar.gz
| |
| − | ../rdkit/boost_1_71_0/
| |
| − | ../rdkit/eigen-3.3.9.tar.gz
| |
| − | ../rdkit/eigen-3.3.9/
| |
| − | ../rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | ../rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@login1 dock]$ git diff sphere.cpp
| |
| − | diff --git a/src/dock/sphere.cpp b/src/dock/sphere.cpp
| |
| − | index 27641d83..5739a67c 100644
| |
| − | --- a/src/dock/sphere.cpp
| |
| − | +++ b/src/dock/sphere.cpp
| |
| − | @@ -111,6 +111,7 @@ read_spheres( string sphere_file_name, SphereVec & spheres )
| |
| − | fclose(sphere_file);
| |
| − |
| |
| − | return num_spheres;
| |
| − | +
| |
| − | }
| |
| − |
| |
| − |
| |
| − | (base) [ehspector@login1 dock]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % mkdir PHYS_561
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % cd PHYS_561
| |
| − | (base) supremestudier@Evans-MBP PHYS_561 % mkdir Readings
| |
| − | (base) supremestudier@Evans-MBP PHYS_561 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login2 ~]$ home
| |
| − | (base) [ehspector@login2 espector]$ class
| |
| − | (base) [ehspector@login2 2025]$ cd
| |
| − | (base) [ehspector@login2 ~]$ ls
| |
| − | class_project miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@login2 ~]$ mv class_project/ AMS_536
| |
| − | (base) [ehspector@login2 ~]$ ls
| |
| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@login2 ~]$ cd AMS_536/
| |
| − | (base) [ehspector@login2 AMS_536]$ ls
| |
| − | (base) [ehspector@login2 AMS_536]$ mkdir class_work
| |
| − | (base) [ehspector@login2 AMS_536]$ mkdir class_project
| |
| − | (base) [ehspector@login2 AMS_536]$ cd ..
| |
| − | (base) [ehspector@login2 ~]$ cd AMS_536/
| |
| − | (base) [ehspector@login2 AMS_536]$ pwd
| |
| − | /gpfs/home/ehspector/AMS_536
| |
| − | (base) [ehspector@login2 AMS_536]$ vi ~/.bashrc
| |
| − | (base) [ehspector@login2 AMS_536]$ source ~/.bashrc
| |
| − | (base) [ehspector@login2 AMS_536]$ home
| |
| − | (base) [ehspector@login2 espector]$ class
| |
| − | (base) [ehspector@login2 AMS_536]$ ls
| |
| − | class_project class_work
| |
| − | (base) [ehspector@login2 AMS_536]$ ls
| |
| − | class_project class_work
| |
| − | (base) [ehspector@login2 AMS_536]$ pwd
| |
| − | /gpfs/home/ehspector/AMS_536
| |
| − | (base) [ehspector@login2 AMS_536]$ cd ..
| |
| − | (base) [ehspector@login2 ~]$ cd ..
| |
| − | (base) [ehspector@login2 home]$ cd ..
| |
| − | (base) [ehspector@login2 gpfs]$ cd projects/
| |
| − | (base) [ehspector@login2 projects]$ ls
| |
| − | ABCD EssigGroup MaoGroup SchedelGroup
| |
| − | AllamGroup FarhadzadehGroup McDonoughGroup SeeligerGroup
| |
| − | AllenGroup FernandezGroup McGrewGroup SehgalGroup
| |
| − | AMS530 FernandezReuterGroup McKinnonGroup ShepsonGroup
| |
| − | AMS536 FrenkelGroup MehmoodGroup SherGroup
| |
| − | AMS598 FutcherGroup MelikerGroup SheridanGroup
| |
| − | AMS691 GenomicsCore MihalacheGroup ShilkrotGroup
| |
| − | Aponte-RiveraGroup GergenGroup MirandaGroup SiegmannGroup
| |
| − | ArmitageGroup glimm MitchellGroup SladeGroup
| |
| − | AssanisGroup GoblerGroup MoellerGroup SmaersGroup
| |
| − | BEE690 GoldbartGroup MofakhamGroup SOC591
| |
| − | BenchmarkGroup HCPGroup MohantyGroup SOC595
| |
| − | BenderGroup HeinzGroup MollProject StanacevicGroup
| |
| − | BernauerGroup HollisterGroup molssi SternGroup
| |
| − | BialkowskaGroup HoltGroup MoutsanidisGroup SyritsynGroup
| |
| − | BIO303 hpc_support MujicaGroup TakeuchiGroup
| |
| − | BluesteinGroup HudsonGroup NadkarniGroup TanGroup
| |
| − | BurguenoGroup IACSPDPGroup NMRPIJodeyGroup TaylorGroup
| |
| − | CalderGroup JiaoGroup NMRPILipshultzGroup TeraChemGroup
| |
| − | CanliGroup JohnsonGroup NMRPIMingNgaiGroup Tesse
| |
| − | CarlsonGroup JonesBozarthGroup NMRPIPicartGroup TestGroup1
| |
| − | CascanteBonillaGroup JonesGroup OjimaGroup ThackerGroup
| |
| − | ChangGroup JonesSkienaGroup OkeomaGroup ThakurGroup
| |
| − | ChapmanGroup KarzaiGroup PadillaGroup ThorneGroup
| |
| − | CheCastaldoGroup KeeGroup PariseGroup TitleGroup
| |
| − | ChenGroup KeeJiaoGroup PercivalGroup TsybychevGroup
| |
| − | ChenXGroup KellyGroup PerlmanGroup VanSnellenbergGroup
| |
| − | CheungGroup KhosronejadGroup PernaGroup VaskaGroup
| |
| − | ChowdhuryGroup KimGroup PicartGroup VeeramahGroup
| |
| − | ChowdhuryRGroup KirylukGroup PiretGroup VitekGroup
| |
| − | ColleGroup KodnerGroup PolakGroup VonDerLindenGroup
| |
| − | CollierGroup KogaGroup PoonGroup VorkasGroup
| |
| − | CSE416 KozakovGroup PowersGroup WangGroup
| |
| − | CSE504 KritzerGroup PSY610 WanGroup
| |
| − | CSE519 KrsticGroup PSY620 WangXGroup
| |
| − | CSE590 KrsticQuantumGroup QuantComp WeinachtGroup
| |
| − | CSE628 KurcGroup RahmeGroup WeinsteinGroup
| |
| − | DAndreaGroup LeungGroup RajputGroup WeissmanGroup
| |
| − | DavalosGroup LevineGroup RambowGroup WilsonGroup
| |
| − | DeLorenzoGroup LiGroup RestGroup WymoreGroup
| |
| − | DengYasarGroup LoverdeGroup ReuterGroup YeGroup
| |
| − | DevarajanGroup LuGroup RiosGroup YouGroup
| |
| − | DheillyGroup LuhmannGroup rizzo ZhangGroup
| |
| − | DillGroup LuoGroup rjh ZhanGroup
| |
| − | DoboliGroup LynchGroup RosatiGroup ZhangYGroup
| |
| − | DubnauGroup MaffeiGroup samples ZhaoGroup
| |
| − | EBH370 MaGroup SampsonCryoEMGroup ZhouGroup
| |
| − | EBH381 MakGroup SampsonGroup ZhouMedAdvGroup
| |
| − | EkblomGroup MallipattuGroup SamulyakGroup ZhuGroup
| |
| − | (base) [ehspector@login2 projects]$ cd AMS536
| |
| − | (base) [ehspector@login2 AMS536]$ cd zzz.programs
| |
| − | (base) [ehspector@login2 zzz.programs]$ ls
| |
| − | amber16 dock6.11 dock6-master.zip plot_footprint_single_magnitude.py
| |
| − | de_novo_anchors dock6.11_alpha dock_directory_arch plot_rmsds_amber
| |
| − | dock6.10 dock6.12 gen-frags-12 VS_libraries
| |
| − | dock6.10_milan dock6.12_ams536 old
| |
| − | (base) [ehspector@login2 zzz.programs]$ cd dock6.12_ams536/
| |
| − | (base) [ehspector@login2 dock6.12_ams536]$ ls
| |
| − | bin docs parameters README.md template_pipeline
| |
| − | developer install README src tutorials
| |
| − | (base) [ehspector@login2 dock6.12_ams536]$ cd bin/
| |
| − | (base) [ehspector@login2 bin]$ ls
| |
| − | am1bcc dock6.mpi multigrid_fp_gen.py sevsolv
| |
| − | amberize_complex espgen nchemgrid_GB showbox
| |
| − | amberize_ligand grid nchemgrid_SA showsphere
| |
| − | amberize_receptor grid-convert parmcal solvgrid
| |
| − | antechamber grid-convrds parmchk solvmap
| |
| − | atomtype make_phimap prepare_amber.pl sphere_selector
| |
| − | bondtype mol2bild.py prepare_rna_amber.pl sphgen
| |
| − | chemgrid mol2.py prepgen teLeap
| |
| − | combine_torenv.py mopac resp tleap
| |
| − | dock6 mopac.sh respgen
| |
| − | (base) [ehspector@login2 bin]$ cd
| |
| − | (base) [ehspector@login2 ~]$ man date
| |
| − | (base) [ehspector@login2 ~]$
| |
| − | (base) [ehspector@login2 ~]$ ls
| |
| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@login2 ~]$ cd ..
| |
| − | (base) [ehspector@login2 home]$ cd ..
| |
| − | (base) [ehspector@login2 gpfs]$ cd projects/AMS536/
| |
| − | (base) [ehspector@login2 AMS536]$ ls
| |
| − | 2017 2019 2021 2023 2025 junk.txt zzz.programs
| |
| − | 2018 2020 2022 2024 get_anchors.py zzz.anchors
| |
| − | (base) [ehspector@login2 AMS536]$ cd 2025/
| |
| − | (base) [ehspector@login2 2025]$ ls
| |
| − | additional_files rotations
| |
| − | (base) [ehspector@login2 2025]$ cd rotations/
| |
| − | (base) [ehspector@login2 rotations]$ ls
| |
| − | aokisamen
| |
| − | (base) [ehspector@login2 rotations]$ cd ..
| |
| − | (base) [ehspector@login2 2025]$ cd ..
| |
| − | (base) [ehspector@login2 AMS536]$ ls
| |
| − | 2017 2019 2021 2023 2025 junk.txt zzz.programs
| |
| − | 2018 2020 2022 2024 get_anchors.py zzz.anchors
| |
| − | (base) [ehspector@login2 AMS536]$ cd 2025/
| |
| − | (base) [ehspector@login2 2025]$ ls
| |
| − | additional_files rotations
| |
| − | (base) [ehspector@login2 2025]$ cd additional_files/
| |
| − | (base) [ehspector@login2 additional_files]$ ls
| |
| − | sample_bashrc_4seawulf.txt sample_slurm_submission.sh test.txt touch.sh
| |
| − | (base) [ehspector@login2 additional_files]$ ls
| |
| − | sample_bashrc_4seawulf.txt sample_slurm_submission.sh test.txt touch.sh
| |
| − | (base) [ehspector@login2 additional_files]$ cd ..
| |
| − | (base) [ehspector@login2 2025]$ ls
| |
| − | additional_files rotations
| |
| − | (base) [ehspector@login2 2025]$ cd ..
| |
| − | (base) [ehspector@login2 AMS536]$ ls
| |
| − | 2017 2019 2021 2023 2025 junk.txt zzz.programs
| |
| − | 2018 2020 2022 2024 get_anchors.py zzz.anchors
| |
| − | (base) [ehspector@login2 AMS536]$ vi junk.txt
| |
| − | (base) [ehspector@login2 AMS536]$ ls
| |
| − | 2017 2019 2021 2023 2025 junk.txt zzz.programs
| |
| − | 2018 2020 2022 2024 get_anchors.py zzz.anchors
| |
| − | (base) [ehspector@login2 AMS536]$ ls
| |
| − | 2017 2019 2021 2023 2025 junk.txt zzz.programs
| |
| − | 2018 2020 2022 2024 get_anchors.py zzz.anchors
| |
| − | (base) [ehspector@login2 AMS536]$ cd 2025
| |
| − | (base) [ehspector@login2 2025]$ ls
| |
| − | additional_files rotations wed_fun.txt
| |
| − | (base) [ehspector@login2 2025]$ ls
| |
| − | additional_files rotations wed_humpday.txt
| |
| − | (base) [ehspector@login2 2025]$ cd
| |
| − | (base) [ehspector@login2 ~]$ cd ../../
| |
| − | (base) [ehspector@login2 gpfs]$ sinfo
| |
| − | PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
| |
| − | gpu up 8:00:00 1 drain sn-nvda5
| |
| − | gpu up 8:00:00 5 alloc sn-nvda[3-4,6-8]
| |
| − | p100 up 1-00:00:00 1 alloc cn-nvidia
| |
| − | gpu-long up 2-00:00:00 1 drain sn-nvda5
| |
| − | gpu-long up 2-00:00:00 5 alloc sn-nvda[3-4,6-8]
| |
| − | gpu-large up 8:00:00 1 drain sn-nvda5
| |
| − | gpu-large up 8:00:00 5 alloc sn-nvda[3-4,6-8]
| |
| − | debug-28core up 1:00:00 1 boot* sn046
| |
| − | debug-28core up 1:00:00 6 drain* sn[030-032,107-109]
| |
| − | debug-28core up 1:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
| |
| − | debug-28core up 1:00:00 12 idle sn[003-004,025-026,043-044,151-156]
| |
| − | extended-28core up 7-00:00:00 1 boot* sn046
| |
| − | extended-28core up 7-00:00:00 6 drain* sn[030-032,107-109]
| |
| − | extended-28core up 7-00:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
| |
| − | extended-28core up 7-00:00:00 12 idle sn[003-004,025-026,043-044,151-156]
| |
| − | large-28core up 8:00:00 1 boot* sn046
| |
| − | large-28core up 8:00:00 6 drain* sn[030-032,107-109]
| |
| − | large-28core up 8:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
| |
| − | large-28core up 8:00:00 12 idle sn[003-004,025-026,043-044,151-156]
| |
| − | long-28core up 2-00:00:00 1 boot* sn046
| |
| − | long-28core up 2-00:00:00 6 drain* sn[030-032,107-109]
| |
| − | long-28core up 2-00:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
| |
| − | long-28core up 2-00:00:00 12 idle sn[003-004,025-026,043-044,151-156]
| |
| − | medium-28core up 12:00:00 1 boot* sn046
| |
| − | medium-28core up 12:00:00 6 drain* sn[030-032,107-109]
| |
| − | medium-28core up 12:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
| |
| − | medium-28core up 12:00:00 12 idle sn[003-004,025-026,043-044,151-156]
| |
| − | short-28core up 4:00:00 1 boot* sn046
| |
| − | short-28core up 4:00:00 6 drain* sn[030-032,107-109]
| |
| − | short-28core up 4:00:00 137 alloc sn[001-002,005-024,027-029,033-042,045,047-106,110-150]
| |
| − | short-28core up 4:00:00 12 idle sn[003-004,025-026,043-044,151-156]
| |
| − | v100 up 1-00:00:00 2 idle sn-nvda[1-2]
| |
| − | (base) [ehspector@login2 gpfs]$ alias
| |
| − | alias class='cd /gpfs/home/ehspector/AMS_536'
| |
| − | alias egrep='egrep --color=auto'
| |
| − | alias fgrep='fgrep --color=auto'
| |
| − | alias grep='grep --color=auto'
| |
| − | alias home='cd /gpfs/projects/rizzo/espector'
| |
| − | alias l.='ls -d .* --color=auto'
| |
| − | alias ll='ls -l --color=auto'
| |
| − | alias ls='ls --color=auto'
| |
| − | alias rd='srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash'
| |
| − | alias vi='vim'
| |
| − | alias which='alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
| |
| − | (base) [ehspector@login2 gpfs]$ class
| |
| − | (base) [ehspector@login2 AMS_536]$ ls
| |
| − | class_project class_work
| |
| − | (base) [ehspector@login2 AMS_536]$ cd class_work/
| |
| − | (base) [ehspector@login2 class_work]$ ls
| |
| − | (base) [ehspector@login2 class_work]$ touch Notes.txt
| |
| − | (base) [ehspector@login2 class_work]$ vi Notes.txt
| |
| − | (base) [ehspector@login2 class_work]$ vi Notes.txt
| |
| − | (base) [ehspector@login2 class_work]$ vi Notes.txt
| |
| − | (base) [ehspector@login2 class_work]$ class
| |
| − | (base) [ehspector@login2 AMS_536]$ cd ..
| |
| − | (base) [ehspector@login2 ~]$ class
| |
| − | (base) [ehspector@login2 AMS_536]$ ls
| |
| − | class_project class_work
| |
| − | (base) [ehspector@login2 AMS_536]$ cd class_work/
| |
| − | (base) [ehspector@login2 class_work]$ ls
| |
| − | Notes.txt
| |
| − | (base) [ehspector@login2 class_work]$ vi Notes.txt
| |
| − | (base) [ehspector@login2 class_work]$ vi Notes.txt
| |
| − | (base) [ehspector@login2 class_work]$ alias
| |
| − | alias class='cd /gpfs/home/ehspector/AMS_536'
| |
| − | alias egrep='egrep --color=auto'
| |
| − | alias fgrep='fgrep --color=auto'
| |
| − | alias grep='grep --color=auto'
| |
| − | alias home='cd /gpfs/projects/rizzo/espector'
| |
| − | alias l.='ls -d .* --color=auto'
| |
| − | alias ll='ls -l --color=auto'
| |
| − | alias ls='ls --color=auto'
| |
| − | alias rd='srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash'
| |
| − | alias vi='vim'
| |
| − | alias which='alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
| |
| − | (base) [ehspector@login2 class_work]$ which dock6
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/bin/dock6
| |
| − | (base) [ehspector@login2 class_work]$ vi Notes.txt
| |
| − | (base) [ehspector@login2 class_work]$ vi ~/.bashrc
| |
| − | (base) [ehspector@login2 class_work]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP PHYS_561 % cd
| |
| − | (base) supremestudier@Evans-MBP ~ % cd Desktop/GradSchool/StonyBrook/Semester/Spring_25/AMS_500
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % ls
| |
| − | Materials
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % mkdir Week_2
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % which python
| |
| − | /Users/supremestudier/anaconda3/bin/python
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % pip install polaris-lib
| |
| − | Collecting polaris-lib
| |
| − | Obtaining dependency information for polaris-lib from https://files.pythonhosted.org/packages/5f/69/3a9d76a53ebc41245755a71968e7789c543fe93cb48fff5b0a0a54aff56b/polaris_lib-0.11.6-py3-none-any.whl.metadata
| |
| − | Downloading polaris_lib-0.11.6-py3-none-any.whl.metadata (5.9 kB)
| |
| − | Collecting authlib (from polaris-lib)
| |
| − | Obtaining dependency information for authlib from https://files.pythonhosted.org/packages/e8/6a/e83a6c04f8c6014c33d97c135782a55370cf60513f8d9f99f1279c7f9c13/Authlib-1.4.1-py2.py3-none-any.whl.metadata
| |
| − | Downloading Authlib-1.4.1-py2.py3-none-any.whl.metadata (3.9 kB)
| |
| − | Collecting boto3<1.36.0 (from polaris-lib)
| |
| − | Obtaining dependency information for boto3<1.36.0 from https://files.pythonhosted.org/packages/65/77/8bbca82f70b062181cf0ae53fd43f1ac6556f3078884bfef9da2269c06a3/boto3-1.35.99-py3-none-any.whl.metadata
| |
| − | Downloading boto3-1.35.99-py3-none-any.whl.metadata (6.7 kB)
| |
| − | Collecting datamol>=0.12.1 (from polaris-lib)
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| − | Collecting scipy (from polaris-lib)
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| − | Building wheels for collected packages: asciitree
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| − | Building wheel for asciitree (setup.py) ... done
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| − | Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5032 sha256=24fc75d0363ae85814cc0078da13ef4692220652876b36186c2bc8fd449fbede
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| − | Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/71/c1/da/23077eb3b87d24d6f3852ed1ed1a1ac2d3c885ad6ebd2b4a07
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| − | Successfully built asciitree
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| − | Installing collected packages: pyroaring, asciitree, typing-extensions, shellingham, selfies, numpy, loguru, importlib-resources, h11, fasteners, deprecated, annotated-types, scipy, rdkit, pydantic-core, numcodecs, httpcore, botocore, zarr, typer, s3transfer, pydantic, httpx, biotraj, authlib, pydantic-settings, datamol, boto3, biotite, fastpdb, polaris-lib
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| − | Attempting uninstall: typing-extensions
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| − | Found existing installation: typing_extensions 4.7.1
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| − | Uninstalling typing_extensions-4.7.1:
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| − | Successfully uninstalled typing_extensions-4.7.1
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| − | Attempting uninstall: numpy
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| − | Found existing installation: numpy 1.24.3
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| − | Found existing installation: scipy 1.11.1
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| − | Successfully uninstalled scipy-1.11.1
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| − | Attempting uninstall: botocore
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| − | Found existing installation: botocore 1.29.76
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| − | Attempting uninstall: pydantic
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| − | Found existing installation: pydantic 1.10.8
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| − | ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
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| − | tables 3.8.0 requires blosc2~=2.0.0, which is not installed.
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| − | numba 0.57.0 requires numpy<1.25,>=1.21, but you have numpy 1.26.4 which is incompatible.
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| − | anaconda-cloud-auth 0.1.3 requires pydantic<2.0, but you have pydantic 2.10.6 which is incompatible.
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| − | aiobotocore 2.5.0 requires botocore<1.29.77,>=1.29.76, but you have botocore 1.35.99 which is incompatible.
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| − | Successfully installed annotated-types-0.7.0 asciitree-0.3.3 authlib-1.4.1 biotite-1.1.0 biotraj-1.2.2 boto3-1.35.99 botocore-1.35.99 datamol-0.12.5 deprecated-1.2.18 fasteners-0.19 fastpdb-1.3.1 h11-0.14.0 httpcore-1.0.7 httpx-0.28.1 importlib-resources-6.5.2 loguru-0.7.3 numcodecs-0.15.0 numpy-1.26.4 polaris-lib-0.11.6 pydantic-2.10.6 pydantic-core-2.27.2 pydantic-settings-2.7.1 pyroaring-1.0.0 rdkit-2024.9.4 s3transfer-0.10.4 scipy-1.15.1 selfies-2.2.0 shellingham-1.5.4 typer-0.15.1 typing-extensions-4.12.2 zarr-2.18.4
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| − | (base) supremestudier@Evans-MBP AMS_500 % polaris login
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| − | [2025-01-31 19:47:50] INFO Your browser has been opened to visit: external_client.py:149
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| − | https://clerk.polarishub.io/oauth/auth
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| − | orize?response_type=code&client_id=agQ
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| − | P2xVM6JqMHvGc&redirect_uri=https%3A%2F
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| − | %2Fpolarishub.io%2Foauth2%2Fcallback&s
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| − | cope=profile+email&state=YEjoNaFiIPI4k
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| − | rv6quFJFVgB09TcYM&code_challenge=QG1cf
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| − | HPgkiyqBUkzPRKUxet5FXo5xZWG21Lh_QXjhSU
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| − | &code_challenge_method=S256
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| − |
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| − | Please enter the authorization token: 013927
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| − | ╭─────────────────────────── Traceback (most recent call last) ────────────────────────────╮
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| − | │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/cli.py:31 in login │
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| − | │ │
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| − | │ 28 │ This CLI will use the OAuth2 protocol to gain token-based access to the Polaris │
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| − | │ 29 │ """ │
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| − | │ 30 │ client = PolarisHubClient(settings=PolarisHubSettings(_env_file=client_env_file │
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| − | │ ❱ 31 │ client.login(auto_open_browser=auto_open_browser, overwrite=overwrite) │
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| − | │ 32 │
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| − | │ 33 │
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| − | │ 34 @app.command(hidden=True) │
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| − | │ │
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| − | │ ╭──────────────────────────────────── locals ─────────────────────────────────────╮ │
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| − | │ │ auto_open_browser = True │ │
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| − | │ │ client = <polaris.hub.client.PolarisHubClient object at 0x1375e8d10> │ │
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| − | │ │ client_env_file = '.env' │ │
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| − | │ │ overwrite = False │ │
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| − | │ ╰─────────────────────────────────────────────────────────────────────────────────╯ │
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| − | │ │
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| − | │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/client.py:249 │
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| − | │ in login │
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| − | │ │
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| − | │ 246 │ │ │ auto_open_browser: Whether to automatically open the browser to visit │
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| − | │ 247 │ │ """ │
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| − | │ 248 │ │ if overwrite or self.token is None or not self.ensure_active_token(): │
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| − | │ ❱ 249 │ │ │ self.external_client.interactive_login(overwrite=overwrite, auto_open_ │
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| − | │ 250 │ │ │ self.token = self.fetch_token() │
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| − | │ 251 │ │ │
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| − | │ 252 │ │ logger.info("You are successfully logged in to the Polaris Hub.") │
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| − | │ │
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| − | │ ╭──────────────────────────────────── locals ─────────────────────────────────────╮ │
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| − | │ │ auto_open_browser = True │ │
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| − | │ │ overwrite = False │ │
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| − | │ │ self = <polaris.hub.client.PolarisHubClient object at 0x1375e8d10> │ │
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| − | │ ╰─────────────────────────────────────────────────────────────────────────────────╯ │
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| − | │ │
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| − | │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/external_client │
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| − | │ .py:158 in interactive_login │
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| − | │ │
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| − | │ 155 │ │ authorization_code = input("Please enter the authorization token: ") │
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| − | │ 156 │ │ │
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| − | │ 157 │ │ # Step 3: Exchange authorization code for an access token │
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| − | │ ❱ 158 │ │ self.fetch_token(code=authorization_code, grant_type="authorization_code") │
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| − | │ 159 │ │ │
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| − | │ 160 │ │ logger.info(f"Successfully authenticated to the Polaris Hub as `{self.user │
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| − | │ 161 │
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| − | │ │
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| − | │ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
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| − | │ │ _ = 'YEjoNaFiIPI4krv6quFJFVgB09TcYM' │ │
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| − | │ │ authorization_code = '013927' │ │
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| − | │ │ authorization_url = 'https://clerk.polarishub.io/oauth/authorize?response_type=cod… │ │
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| − | │ │ auto_open_browser = True │ │
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| − | │ │ overwrite = False │ │
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| − | │ │ self = <polaris.hub.external_client.ExternalAuthClient object at │ │
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| − | │ │ 0x1356cad90> │ │
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| − | │ │ token_is_valid = False │ │
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| − | │ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
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| − | │ │
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| − | │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/polaris/hub/external_client │
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| − | │ .py:74 in fetch_token │
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| − | │ │
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| − | │ 71 │ def fetch_token(self, **kwargs) -> dict: │
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| − | │ 72 │ │ """Light wrapper to automatically pass in the right URL""" │
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| − | │ 73 │ │ try: │
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| − | │ ❱ 74 │ │ │ return super().fetch_token( │
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| − | │ 75 │ │ │ │ url=self.settings.token_fetch_url, code_verifier=self.code_verifie │
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| − | │ 76 │ │ │ ) │
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| − | │ 77 │ │ except OAuth2Error as error: │
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| − | │ │
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| − | │ ╭──────────────────────────────────── locals ─────────────────────────────────────╮ │
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| − | │ │ kwargs = {'code': '013927', 'grant_type': 'authorization_code'} │ │
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| − | │ │ self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90> │ │
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| − | │ ╰─────────────────────────────────────────────────────────────────────────────────╯ │
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| − | │ │
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| − | │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:21 │
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| − | │ 7 in fetch_token │
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| − | │ │
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| − | │ 214 │ │ if url is None: │
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| − | │ 215 │ │ │ url = self.metadata.get('token_endpoint') │
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| − | │ 216 │ │ │
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| − | │ ❱ 217 │ │ return self._fetch_token( │
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| − | │ 218 │ │ │ url, body=body, auth=auth, method=method, │
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| − | │ 219 │ │ │ headers=headers, **session_kwargs │
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| − | │ 220 │ │ ) │
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| − | │ │
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| − | │ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
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| − | │ │ auth = <authlib.integrations.httpx_client.oauth2_client.OAuth2Cli… │ │
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| − | │ │ object at 0x136f50190> │ │
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| − | │ │ authorization_response = None │ │
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| − | │ │ body = 'grant_type=authorization_code&redirect_uri=https%3A%2F%2F… │ │
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| − | │ │ grant_type = 'authorization_code' │ │
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| − | │ │ headers = { │ │
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| − | │ │ │ 'Accept': 'application/json', │ │
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| − | │ │ │ 'Content-Type': │ │
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| − | │ │ 'application/x-www-form-urlencoded;charset=UTF-8' │ │
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| − | │ │ } │ │
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| − | │ │ kwargs = { │ │
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| − | │ │ │ 'code_verifier': │ │
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| − | │ │ 'S2qmBfN72W2onFO2So06MzNLUB8yVXmHmp4m9xisHaIUA9zU', │ │
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| − | │ │ │ 'code': '013927' │ │
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| − | │ │ } │ │
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| − | │ │ method = 'POST' │ │
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| − | │ │ self = <polaris.hub.external_client.ExternalAuthClient object at │ │
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| − | │ │ 0x1356cad90> │ │
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| − | │ │ session_kwargs = {} │ │
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| − | │ │ state = None │ │
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| − | │ │ url = 'https://clerk.polarishub.io/oauth/token' │ │
| |
| − | │ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
| |
| − | │ │
| |
| − | │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:37 │
| |
| − | │ 9 in _fetch_token │
| |
| − | │ │
| |
| − | │ 376 │ │ for hook in self.compliance_hook['access_token_response']: │
| |
| − | │ 377 │ │ │ resp = hook(resp) │
| |
| − | │ 378 │ │ │
| |
| − | │ ❱ 379 │ │ return self.parse_response_token(resp) │
| |
| − | │ 380 │ │
| |
| − | │ 381 │ def _refresh_token(self, url, refresh_token=None, body='', headers=None, │
| |
| − | │ 382 │ │ │ │ │ auth=None, **kwargs): │
| |
| − | │ │
| |
| − | │ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
| |
| − | │ │ auth = <authlib.integrations.httpx_client.oauth2_client.OAuth2ClientAuth object │ │
| |
| − | │ │ at 0x136f50190> │ │
| |
| − | │ │ body = 'grant_type=authorization_code&redirect_uri=https%3A%2F%2Fpolarishub.io%2… │ │
| |
| − | │ │ headers = { │ │
| |
| − | │ │ │ 'Accept': 'application/json', │ │
| |
| − | │ │ │ 'Content-Type': 'application/x-www-form-urlencoded;charset=UTF-8' │ │
| |
| − | │ │ } │ │
| |
| − | │ │ kwargs = {} │ │
| |
| − | │ │ method = 'POST' │ │
| |
| − | │ │ resp = <Response [401 Unauthorized]> │ │
| |
| − | │ │ self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90> │ │
| |
| − | │ │ url = 'https://clerk.polarishub.io/oauth/token' │ │
| |
| − | │ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
| |
| − | │ │
| |
| − | │ /Users/supremestudier/anaconda3/lib/python3.11/site-packages/authlib/oauth2/client.py:35 │
| |
| − | │ 5 in parse_response_token │
| |
| − | │ │
| |
| − | │ 352 │ │ │
| |
| − | │ 353 │ │ token = resp.json() │
| |
| − | │ 354 │ │ if 'error' in token: │
| |
| − | │ ❱ 355 │ │ │ raise self.oauth_error_class( │
| |
| − | │ 356 │ │ │ │ error=token['error'], │
| |
| − | │ 357 │ │ │ │ description=token.get('error_description') │
| |
| − | │ 358 │ │ │ ) │
| |
| − | │ │
| |
| − | │ ╭─────────────────────────────────────── locals ───────────────────────────────────────╮ │
| |
| − | │ │ resp = <Response [401 Unauthorized]> │ │
| |
| − | │ │ self = <polaris.hub.external_client.ExternalAuthClient object at 0x1356cad90> │ │
| |
| − | │ │ token = { │ │
| |
| − | │ │ │ 'error': 'invalid_grant', │ │
| |
| − | │ │ │ 'error_description': 'The provided authorization grant (e.g., │ │
| |
| − | │ │ authorization code, resource owner crede'+156 │ │
| |
| − | │ │ } │ │
| |
| − | │ ╰──────────────────────────────────────────────────────────────────────────────────────╯ │
| |
| − | ╰──────────────────────────────────────────────────────────────────────────────────────────╯
| |
| − | OAuthError: invalid_grant: The provided authorization grant (e.g., authorization code,
| |
| − | resource owner credentials) or refresh token is invalid, expired, revoked, does not match
| |
| − | the redirection URI used in the authorization request, or was issued to another client
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % polaris login
| |
| − | [2025-01-31 19:49:32] INFO Your browser has been opened to visit: external_client.py:149
| |
| − | https://clerk.polarishub.io/oauth/auth
| |
| − | orize?response_type=code&client_id=agQ
| |
| − | P2xVM6JqMHvGc&redirect_uri=https%3A%2F
| |
| − | %2Fpolarishub.io%2Foauth2%2Fcallback&s
| |
| − | cope=profile+email&state=qo1ea4ucZsaZS
| |
| − | OGFfAWK47Skq0G4jU&code_challenge=irfzd
| |
| − | YmRLZliQeiwg2GQYa156QMYqb4zXHNXQJFb0pE
| |
| − | &code_challenge_method=S256
| |
| − |
| |
| − | Please enter the authorization token: MTLLNZK2ZWETMDBMMY0ZMGU5LWJJYZKTZWI5MZYWMDHIOTCZ
| |
| − | [2025-01-31 19:49:45] INFO Successfully authenticated to the external_client.py:160
| |
| − | Polaris Hub as
| |
| − | `evan.spector@stonybrook.edu`! 🎉
| |
| − | [2025-01-31 19:49:46] INFO You are successfully logged in to the Polaris client.py:252
| |
| − | Hub.
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | (base) [ehspector@login1 ~]$ home
| |
| − | (base) [ehspector@login1 espector]$ module list
| |
| − | Currently Loaded Modulefiles:
| |
| − | 1) slurm/17.11.12 2) shared 3) gcc/13.2.0 4) mvapich2/gcc13.2/2.3.7 5) gcc-stack
| |
| − | (base) [ehspector@login1 espector]$ module load git
| |
| − | WARNING: $PATH does not agree with $PATH_modshare counter. The following directories' usage counters were adjusted to match. Note that this may mean that module unloading may not work correctly.
| |
| − | /cm/local/apps/environment-modules/4.0.0//bin
| |
| − | (base) [ehspector@login1 espector]$ git diff
| |
| − | warning: Not a git repository. Use --no-index to compare two paths outside a working tree
| |
| − | usage: git diff --no-index [<options>] <path> <path>
| |
| − |
| |
| − | Diff output format options
| |
| − | -p, --patch generate patch
| |
| − | -s, --no-patch suppress diff output
| |
| − | -u generate patch
| |
| − | -U, --unified[=<n>] generate diffs with <n> lines context
| |
| − | -W, --function-context
| |
| − | generate diffs with <n> lines context
| |
| − | --raw generate the diff in raw format
| |
| − | --patch-with-raw synonym for '-p --raw'
| |
| − | --patch-with-stat synonym for '-p --stat'
| |
| − | --numstat machine friendly --stat
| |
| − | --shortstat output only the last line of --stat
| |
| − | -X, --dirstat[=<param1,param2>...]
| |
| − | output the distribution of relative amount of changes for each sub-directory
| |
| − | --cumulative synonym for --dirstat=cumulative
| |
| − | --dirstat-by-file[=<param1,param2>...]
| |
| − | synonym for --dirstat=files,param1,param2...
| |
| − | --check warn if changes introduce conflict markers or whitespace errors
| |
| − | --summary condensed summary such as creations, renames and mode changes
| |
| − | --name-only show only names of changed files
| |
| − | --name-status show only names and status of changed files
| |
| − | --stat[=<width>[,<name-width>[,<count>]]]
| |
| − | generate diffstat
| |
| − | --stat-width <width> generate diffstat with a given width
| |
| − | --stat-name-width <width>
| |
| − | generate diffstat with a given name width
| |
| − | --stat-graph-width <width>
| |
| − | generate diffstat with a given graph width
| |
| − | --stat-count <count> generate diffstat with limited lines
| |
| − | --compact-summary generate compact summary in diffstat
| |
| − | --binary output a binary diff that can be applied
| |
| − | --full-index show full pre- and post-image object names on the "index" lines
| |
| − | --color[=<when>] show colored diff
| |
| − | --ws-error-highlight <kind>
| |
| − | highlight whitespace errors in the 'context', 'old' or 'new' lines in the diff
| |
| − | -z do not munge pathnames and use NULs as output field terminators in --raw or --numstat
| |
| − | --abbrev[=<n>] use <n> digits to display object names
| |
| − | --src-prefix <prefix>
| |
| − | show the given source prefix instead of "a/"
| |
| − | --dst-prefix <prefix>
| |
| − | show the given destination prefix instead of "b/"
| |
| − | --line-prefix <prefix>
| |
| − | prepend an additional prefix to every line of output
| |
| − | --no-prefix do not show any source or destination prefix
| |
| − | --inter-hunk-context <n>
| |
| − | show context between diff hunks up to the specified number of lines
| |
| − | --output-indicator-new <char>
| |
| − | specify the character to indicate a new line instead of '+'
| |
| − | --output-indicator-old <char>
| |
| − | specify the character to indicate an old line instead of '-'
| |
| − | --output-indicator-context <char>
| |
| − | specify the character to indicate a context instead of ' '
| |
| − |
| |
| − | Diff rename options
| |
| − | -B, --break-rewrites[=<n>[/<m>]]
| |
| − | break complete rewrite changes into pairs of delete and create
| |
| − | -M, --find-renames[=<n>]
| |
| − | detect renames
| |
| − | -D, --irreversible-delete
| |
| − | omit the preimage for deletes
| |
| − | -C, --find-copies[=<n>]
| |
| − | detect copies
| |
| − | --find-copies-harder use unmodified files as source to find copies
| |
| − | --no-renames disable rename detection
| |
| − | --rename-empty use empty blobs as rename source
| |
| − | --follow continue listing the history of a file beyond renames
| |
| − | -l <n> prevent rename/copy detection if the number of rename/copy targets exceeds given limit
| |
| − |
| |
| − | Diff algorithm options
| |
| − | --minimal produce the smallest possible diff
| |
| − | -w, --ignore-all-space
| |
| − | ignore whitespace when comparing lines
| |
| − | -b, --ignore-space-change
| |
| − | ignore changes in amount of whitespace
| |
| − | --ignore-space-at-eol
| |
| − | ignore changes in whitespace at EOL
| |
| − | --ignore-cr-at-eol ignore carrier-return at the end of line
| |
| − | --ignore-blank-lines ignore changes whose lines are all blank
| |
| − | -I, --ignore-matching-lines <regex>
| |
| − | ignore changes whose all lines match <regex>
| |
| − | --indent-heuristic heuristic to shift diff hunk boundaries for easy reading
| |
| − | --patience generate diff using the "patience diff" algorithm
| |
| − | --histogram generate diff using the "histogram diff" algorithm
| |
| − | --diff-algorithm <algorithm>
| |
| − | choose a diff algorithm
| |
| − | --anchored <text> generate diff using the "anchored diff" algorithm
| |
| − | --word-diff[=<mode>] show word diff, using <mode> to delimit changed words
| |
| − | --word-diff-regex <regex>
| |
| − | use <regex> to decide what a word is
| |
| − | --color-words[=<regex>]
| |
| − | equivalent to --word-diff=color --word-diff-regex=<regex>
| |
| − | --color-moved[=<mode>]
| |
| − | moved lines of code are colored differently
| |
| − | --color-moved-ws <mode>
| |
| − | how white spaces are ignored in --color-moved
| |
| − |
| |
| − | Other diff options
| |
| − | --relative[=<prefix>]
| |
| − | when run from subdir, exclude changes outside and show relative paths
| |
| − | -a, --text treat all files as text
| |
| − | -R swap two inputs, reverse the diff
| |
| − | --exit-code exit with 1 if there were differences, 0 otherwise
| |
| − | --quiet disable all output of the program
| |
| − | --ext-diff allow an external diff helper to be executed
| |
| − | --textconv run external text conversion filters when comparing binary files
| |
| − | --ignore-submodules[=<when>]
| |
| − | ignore changes to submodules in the diff generation
| |
| − | --submodule[=<format>]
| |
| − | specify how differences in submodules are shown
| |
| − | --ita-invisible-in-index
| |
| − | hide 'git add -N' entries from the index
| |
| − | --ita-visible-in-index
| |
| − | treat 'git add -N' entries as real in the index
| |
| − | -S <string> look for differences that change the number of occurrences of the specified string
| |
| − | -G <regex> look for differences that change the number of occurrences of the specified regex
| |
| − | --pickaxe-all show all changes in the changeset with -S or -G
| |
| − | --pickaxe-regex treat <string> in -S as extended POSIX regular expression
| |
| − | -O <file> control the order in which files appear in the output
| |
| − | --rotate-to <path> show the change in the specified path first
| |
| − | --skip-to <path> skip the output to the specified path
| |
| − | --find-object <object-id>
| |
| − | look for differences that change the number of occurrences of the specified object
| |
| − | --diff-filter [(A|C|D|M|R|T|U|X|B)...[*]]
| |
| − | select files by diff type
| |
| − | --output <file> output to a specific file
| |
| − |
| |
| − | (base) [ehspector@login1 espector]$ git status
| |
| − | fatal: not a git repository (or any parent up to mount point /)
| |
| − | Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
| |
| − | (base) [ehspector@login1 espector]$ git branch
| |
| − | fatal: not a git repository (or any parent up to mount point /)
| |
| − | Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
| |
| − | (base) [ehspector@login1 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login1 espector]$ module list
| |
| − | Currently Loaded Modulefiles:
| |
| − | 1) slurm/17.11.12 3) gcc/13.2.0 5) gcc-stack
| |
| − | 2) shared 4) mvapich2/gcc13.2/2.3.7 6) git/2.36.2
| |
| − | (base) [ehspector@login1 espector]$ history
| |
| − | 9 make rdkit
| |
| − | 10 modue list
| |
| − | 11 module list
| |
| − | 12 module unload gcc
| |
| − | 13 module list
| |
| − | 14 module unload mvapich2/gcc13.2/2.3.7
| |
| − | 15 module unload gcc-stack
| |
| − | 16 module list
| |
| − | 17 module load gcc/7.2.0
| |
| − | 18 which gcc
| |
| − | 19 make rdkitclean
| |
| − | 20 make rdkit
| |
| − | 21 srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
| |
| − | 22 vi ~/.bashrc
| |
| − | 23 module list
| |
| − | 24 ls
| |
| − | 25 source ~/.bashrc
| |
| − | 26 module list
| |
| − | 27 ls
| |
| − | 28 vi ~/.bashrc
| |
| − | 29 make clean
| |
| − | 30 ./configure gnu.rdkit
| |
| − | 31 make dock
| |
| − | 32 srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
| |
| − | 33 home
| |
| − | 34 cd RDKit/gas/
| |
| − | 35 ls
| |
| − | 36 sbatch 4s0v_filter.slurm
| |
| − | 37 vi 4s0v_filter.slurm
| |
| − | 38 sbatch 4s0v_filter.slurm
| |
| − | 39 squeue -u ehspector
| |
| − | 40 vi 4s0v_filter.slurm
| |
| − | 41 squeue -u ehspector
| |
| − | 42 cd ..
| |
| − | 43 cd 4s0v/
| |
| − | 44 cd GA
| |
| − | 45 ls
| |
| − | 46 cd 4s0v_GA_results/
| |
| − | 47 ls
| |
| − | 48 vi 4s0v_GA_output.restart0000.mol2
| |
| − | 49 vi 4s0v_GA_output.restart0001.mol2
| |
| − | 50 cd ..
| |
| − | 51 ls
| |
| − | 52 cd virtual_screening/
| |
| − | 53 ls
| |
| − | 54 vi virtual.in
| |
| − | 55 squeue -u ehspector
| |
| − | 56 cd ..
| |
| − | 57 cd RDKit/gas/
| |
| − | 58 ls
| |
| − | 59 vi filter_out.txt
| |
| − | 60 cd ..
| |
| − | 61 cd 4s0v/gas_teiger/
| |
| − | 62 ls
| |
| − | 63 touch gas_rdkit
| |
| − | 64 dock6 -i gas_rdkit
| |
| − | 65 which dock
| |
| − | 66 vi ~/.bashrc
| |
| − | 67 source ~/.bashrc
| |
| − | 68 which dock
| |
| − | 69 which rdkit
| |
| − | 70 source ~/.bashrc
| |
| − | 71 which dock6
| |
| − | 72 which dock6.rdkit
| |
| − | 73 vi ~/.bashrc
| |
| − | 74 source ~/.bashrc
| |
| − | 75 which dock6.rdkit
| |
| − | 76 ls
| |
| − | 77 dock6.rdkit -i gas_rdkit
| |
| − | 78 rm gas_rdkit
| |
| − | 79 cd ..
| |
| − | 80 cd RDKit/
| |
| − | 81 cd gas
| |
| − | 82 sbatch 4s0v_filter.slurm
| |
| − | 83 squeue -u ehspector
| |
| − | 84 ls
| |
| − | 85 squeue -u ehspector
| |
| − | 86 ls
| |
| − | 87 vi output_scored.mol2
| |
| − | 88 squeue -u ehspector
| |
| − | 89 vi output_scored.mol2
| |
| − | 90 cd ..
| |
| − | 91 vi output_scored.mol2
| |
| − | 92 cd ..
| |
| − | 93 cd 4s0v/
| |
| − | 94 ls
| |
| − | 95 cd GA_data/
| |
| − | 96 ls
| |
| − | 97 cd ..
| |
| − | 98 cd GA
| |
| − | 99 ls
| |
| − | 100 cd ..
| |
| − | 101 cd gas_teiger/
| |
| − | 102 ls
| |
| − | 103 touch gas_rd.in
| |
| − | 104 dock6.rdkit gas_rd.in
| |
| − | 105 cd ..
| |
| − | 106 cd gas_teiger/
| |
| − | 107 dock6 -i gas_rd.in
| |
| − | 108 rm gas_rd.in
| |
| − | 109 cd ..
| |
| − | 110 ls
| |
| − | 111 cd ..
| |
| − | 112 cd builds/alpha_branch/src/dock
| |
| − | 113 vi filter.cpp
| |
| − | 114 cd ..
| |
| − | 115 cd install/
| |
| − | 116 make clean
| |
| − | 117 make dock
| |
| − | 118 ls
| |
| − | 119 ./configure
| |
| − | 120 ./configure gnu
| |
| − | 121 make -i distclean
| |
| − | 122 make dock
| |
| − | 123 ./configure
| |
| − | 124 ./configure gnu
| |
| − | 125 make clean
| |
| − | 126 ./configure gnu
| |
| − | 127 make dock
| |
| − | 128 module unload gcc/7.2.0
| |
| − | 129 module load gcc-stack
| |
| − | 130 make dock
| |
| − | 131 cd ..
| |
| − | 132 cd ../..
| |
| − | 133 ls
| |
| − | 134 cd 4s0v/gas_teiger/
| |
| − | 135 ls
| |
| − | 136 dock6 -i gas.in
| |
| − | 137 ls
| |
| − | 138 vi gas.out_scored.mol2
| |
| − | 139 cd ..
| |
| − | 140 cd builds/alpha_branch/src/dock
| |
| − | 141 ls
| |
| − | 142 vi filter.cpp
| |
| − | 143 cd ../..
| |
| − | 144 cd install/
| |
| − | 145 make clean
| |
| − | 146 make dock
| |
| − | 147 cd ../../..
| |
| − | 148 cd 4s0v/gas_teiger/
| |
| − | 149 dock6 -i gas.in
| |
| − | 150 ls
| |
| − | 151 vi gas.out_scored.mol2
| |
| − | 152 cd ../..
| |
| − | 153 cd builds/alpha_branch/src/dock
| |
| − | 154 vi filter.cpp
| |
| − | 155 cd ..]
| |
| − | 156 cd ..
| |
| − | 157 cd install/
| |
| − | 158 make clean
| |
| − | 159 make dock
| |
| − | 160 make clean
| |
| − | 161 srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
| |
| − | 162 home
| |
| − | 163 module list
| |
| − | 164 cd 4s0v/
| |
| − | 165 ls
| |
| − | 166 cd GA
| |
| − | 167 ls
| |
| − | 168 squeue -u ehspector
| |
| − | 169 ls
| |
| − | 170 cd 4s0v_GA_results/
| |
| − | 171 ls
| |
| − | 172 cd ..
| |
| − | 173 ls
| |
| − | 174 cd gas_test/
| |
| − | 175 ls
| |
| − | 176 vi test.in
| |
| − | 177 dock6 -i test.in
| |
| − | 178 ls
| |
| − | 179 vi test.in
| |
| − | 180 dock6 -i test.in
| |
| − | 181 cd ..
| |
| − | 182 cp 4s0v/GA/4s0v_GA_results/4s0v_GA.in gas_test/
| |
| − | 183 ls
| |
| − | 184 cd gas_test/
| |
| − | 185 ls
| |
| − | 186 mkdir gas_f_test
| |
| − | 187 ls
| |
| − | 188 cd ..
| |
| − | 189 cp 4s0v/GA/4s0v_GA_results/4s0v_GA.slurm gas_test/gas_f_test/
| |
| − | 190 cd gas_test/
| |
| − | 191 mv gas_f_test/4s0v_GA.slurm gas_test
| |
| − | 192 ls
| |
| − | 193 cd gas_f_test/
| |
| − | 194 ls
| |
| − | 195 cd ..
| |
| − | 196 mv gas_test 4s0v_GA.slurm
| |
| − | 197 ls
| |
| − | 198 vi 4s0v_GA.slurm
| |
| − | 199 vi 4s0v_GA.in
| |
| − | 200 cd ..
| |
| − | 201 cd 4s0v/GA
| |
| − | 202 ls
| |
| − | 203 cd 4s0v_fraglib/
| |
| − | 204 pwd
| |
| − | 205 cd ..
| |
| − | 206 cd gas_test/
| |
| − | 207 ls
| |
| − | 208 vi 4s0v_GA.in
| |
| − | 209 cd ..
| |
| − | 210 ls
| |
| − | 211 cd ..
| |
| − | 212 ls
| |
| − | 213 cd zzz.programs/
| |
| − | 214 ls
| |
| − | 215 cd ..
| |
| − | 216 cd espector/
| |
| − | 217 ls
| |
| − | 218 cd gas_test/
| |
| − | 219 ls
| |
| − | 220 vi 4s0v_GA.in
| |
| − | 221 vi 4s0v_GA.slurm
| |
| − | 222 vi 4s0v_GA.
| |
| − | 223 vi 4s0v_GA.in
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| − | 225 sbatch 4s0v_GA.slurm
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| − | 226 squeue -u ehspector
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| − | 227 exit
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| − | 228 squeue -u ehspector
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| − | 229 exit
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| − | 230 home
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| − | 231 squeue -u ehspector
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| − | 232 exir
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| − | 233 exit
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| − | 235 squeue -u ehspector
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| − | 236 ls
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| − | 237 cd gas_test/
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| − | 242 vi GA.txt
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| − | 245 cd gas_test/
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| − | 247 vi 4s0v_GA.in
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| − | 248 cd ..
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| − | 249 cd 4s0v/GA
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| − | 250 ls
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| − | 251 cd 4s0v_
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| − | 252 cd 4s0v_fraglib/
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| − | 256 cd 4s0v_GA_results/
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| − | 258 vi 4s0v_GA.in
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| − | 261 ls
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| − | 265 cd gas_test/
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| − | 266 ls
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| − | 267 vi 4s0v_GA.in
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| − | 269 squeue -u ehspector
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| − | 270 home
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| − | 271 cd gas_test/
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| − | 272 ls
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| − | 273 vi GA.txt
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| − | 274 vi 4s0v_GA.in
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| − | 276 vimdiff 4s0v/GA/4s0v_GA_results/4s0v_GA.in gas_test/4s0v_GA.in
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| − | 277 cd gas_test/
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| − | 278 vi 4s0v_GA.in
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| − | 279 sbatch 4s0v_GA.slurm
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| − | 280 squeue -u ehspector
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| − | 281 ls
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| − | 282 vi GA.txt
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| − | 283 vi 4s0v_GA.in
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| − | 284 vi GA.txt
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| − | 285 module list
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| − | 286 cd ..
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| − | 287 cd builds/
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| − | 288 cd alpha_branch/src/dock
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| − | 289 make clean
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| − | 290 make dock
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| − | 291 home
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| − | 292 ls
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| − | 293 cd RDKit/
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| − | 294 ls
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| − | 295 vi filter.in
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| − | 296 cd
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| − | 297 home
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| − | 298 ls
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| − | 299 cd RDKit/
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| − | 307 vi filter.in
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| − | 309 cd ..
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| − | 310 home
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| − | 311 ls
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| − | 312 cd builds/alpha_branch/src/h
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| − | 313 cd builds/alpha_branch/src/dock
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| − | 314 cd ..
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| − | 315 cd install
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| − | 316 history
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| − | 317 cd ..
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| − | 318 cd install/
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| − | 319 ./configure gnu
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| − | 323 ls
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| − | 328 vi 4s0v_GA.in
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| − | 329 vi 4s0v_GA.slurm
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| − | 330 sbatch 4s0v_GA.slurm
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| − | 331 squeue -u ehspector
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| − | 332 ls
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| − | 333 vi GA.txt \
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| − | 334 vi GA.txt
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| − | 335 exit
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| − | 336 home
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| − | 337 ls
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| − | 338 cd RDKit/
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| − | 339 ls
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| − | 340 cd gas/
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| − | 343 cd gas_test/
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| − | 344 ls
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| − | 345 sbatch 4s0v_GA.slurm
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| − | 346 vi 4s0v_GA.slurm
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| − | 347 sbatch 4s0v_GA.slurm
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| − | 348 squeue -u ehspector
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| − | 349 ls
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| − | 350 vi GA.txt
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| − | 351 home
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| − | 352 cd builds/alpha_branch/install/
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| − | 353 make clean
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| − | 354 ./configure gnu
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| − | 355 cd ./install
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| − | 356 make dock
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| − | 357 cd ..
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| − | 358 module list
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| − | 359 module load gcc-stack
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| − | 360 module list
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| − | 361 cd ..
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| − | 362 ls
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| − | 363 cd gas_test/
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| − | 364 ls
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| − | 365 sbatch 4s0v_GA.slurm
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| − | 366 squeue -u ehspector
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| − | 367 ls
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| − | 368 vi 4s0v_GA_output.restart0000.mol2
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| − | 369 ls
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| − | 370 module list
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| − | 371 ls
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| − | 372 squeue -u ehspector
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| − | 373 ls
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| − | 374 squeue -u ehspector
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| − | 375 exit
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| − | 376 home
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| − | 377 ls
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| − | 378 cd gas_test/
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| − | 379 ls
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| − | 380 cd ..
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| − | 381 cp 4s0v/gas_teiger/gas.in gas_test/gas_f_test/
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| − | 382 cd gas_test/gas_f_test/
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| − | 383 ls
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| − | 384 vi gas.in
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| − | 385 cd ..
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| − | 386 pwd
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| − | 387 cd gas_f_test/
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| − | 388 vi gas.in
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| − | 389 dock6 -i gas.in -o gas_0.out
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| − | 390 ls
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| − | 392 vi gas_0.out
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| − | 398 vimdiff 4s0v_GA_output.restart0000.mol2 gas_f_test/gas.out_scored.mol2
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| − | 399 cd ..
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| − | 400 cd gas_test/
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| − | 404 mv gas.out_scored.mol2 gas_0.out_scored.mol2
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| − | 405 ls
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| − | 406 vi gas.in
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| − | 407 mv gas.in gas_1.in
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| − | 408 dock6 -i gas_1.in -o gas_1.out
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| − | 409 ls
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| − | 410 mv gas.out_scored.mol2 gas_1.out_scored.mol2
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| − | 411 vi gas_1.out_scored.mol2
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| − | 412 cd ..
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| − | 413 vi 4s0v_GA_output.restart0001.mol2
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| − | 414 vi 4s0v_GA_output.restart0050.mol2
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| − | 415 cd gas_f_test/
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| − | 416 ls
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| − | 417 cp gas_1.in gas_50.out
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| − | 418 mv gas_50.out gas_50.in
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| − | 419 vi gas_50.in
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| − | 420 dock6 -i gas_50.in -o gas_50.out
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| − | 421 ls
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| − | 422 mv gas.out_scored.mol2 gas_50.out_scored.mol2
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| − | 423 vi gas_50.out_scored.mol2
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| − | 424 cd ..
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| − | 425 vi 4s0v_GA_output.restart0050.mol2
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| − | 426 cd gas_f_test/
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| − | 427 vi gas_50.out_scored.mol2
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| − | 428 cd ..
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| − | 429 mkdir gas_RD_tes
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| − | 430 mv gas_RD_tes/ gas_RD_Test/
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| − | 431 ls
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| − | 432 exit
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| − | 433 make clean
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| − | 434 make dock
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| − | 435 cd ..
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| − | 436 ls
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| − | 437 home
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| − | 438 ls
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| − | 439 cd RDKit/
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| − | 440 ls
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| − | 441 vi filter
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| − | 442 vi filter.in
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| − | 443 cd gas
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| − | 444 ls
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| − | 445 vi filter.
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| − | 446 vi filter.in
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| − | 448 cd RDKit/
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| − | 449 cd gas/
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| − | 450 ls
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| − | 451 cd gas_test/
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| − | 452 ls
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| − | 453 cd ..
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| − | 454 cp RDKit/gas/filter.in gas_test/gas_RD_Test/
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| − | 455 cd RDKit/
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| − | 456 ls
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| − | 457 vi 4s0v_filter.slurm
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| − | 458 cd ..
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| − | 459 home
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| − | 460 cd gas_test/
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| − | 461 ls
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| − | 462 cd gas_RD_Test/
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| − | 463 ls
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| − | 464 cd ..
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| − | 465 cd gas_RD_Test/
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| − | 466 ls
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| − | 467 cd ..
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| − | 468 cd gas_f_test/
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| − | 469 ls
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| − | 470 vi gas_0.in
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| − | 471 vi gas_1.in
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| − | 472 cd ..
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| − | 473 cd gas_RD_Test/
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| − | 474 vi filter.in
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| − | 475 mv filter.in gas.in
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| − | 476 dock6.rdkit -i gas.in -o gas.out
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| − | 477 ls
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| − | 478 vi output_scored.mol2
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| − | 479 ls
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| − | 480 vi gas.out
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| − | 481 vi gas.in
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| − | 482 dock6.rdkit -i gas.in -o gas.out
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| − | 483 ls
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| − | 484 vi gas.out
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| − | 485 vi gas.in
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| − | 486 exit
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| − | 487 home
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| − | 488 cd builds/alpha_branch/install/
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| − | 489 make clean
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| − | 490 ls
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| − | 491 ./configure gnu.rdkit
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| − | 492 make dock
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| − | 493 module list
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| − | 494 srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
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| − | 495 exit
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| − | 496 dock6.rdkit -i gas_50.in -o gas_50.out
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| − | 497 ls
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| − | 498 grep -wc MOLECULE *.mol2
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| − | 499 diff output_scored.mol2 ../4s0v_GA_output.restart0050.mol2
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| − | 500 diff output_scored.mol2 ../4s0v_GA_output.restart0050.mol2 > diff.out
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| − | 501 vi diff.out
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| − | 502 vi output_scored.mol2
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| − | 503 cd ..
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| − | 504 cd gas_f_test/
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| − | 505 ls
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| − | 506 grep -wc MOLECULE gas_50.out_scored.mol2
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| − | 507 diff gas_50.out_scored.mol2 ../4s0v_GA_output.restart0050.mol2 > diff.out
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| − | 508 vi diff.out
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| − | 509 home
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| − | 510 vi ~/.bashrc
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| − | 511 source ~/.bashrc
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| − | 512 exit
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| − | 513 home
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| − | 514 cd gas_test/
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| − | 515 ls
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| − | 517 ls
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| − | 518 vi gas.out
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| − | 520 vi gas.in
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| − | 521 vi output_scored.mol2
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| − | 522 ls
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| − | 523 cd ..
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| − | 524 ls
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| − | 525 grep -wc MOLECULE 4s0v_GA_output.restart0001.mol2
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| − | 526 cd ..
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| − | 527 ls
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| − | 528 cd gas_test/
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| − | 529 ls
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| − | 530 cd gas_RD_Test/
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| − | 531 ls
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| − | 532 vi gas.out
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| − | 533 vi output_rejected.mol2
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| − | 534 cd ..
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| − | 535 vimdiff 4s0v_GA_output.restart0001.mol2 gas_RD_Test/output_scored.mol2
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| − | 536 diff 4s0v_GA_output.restart0001.mol2 gas_RD_Test/output_scored.mol2
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| − | 537 diff -y 4s0v_GA_output.restart0001.mol2 gas_RD_Test/output_scored.mol2
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| − | 538 cd gas_RD_Test/
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| − | 539 ls
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| − | 540 cp gas.in gas_50.in
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| − | 541 vi gas_50.in
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| − | 542 dock6.rdkit -i gas_50.in -o gas_50.out
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| − | 543 dock6.rdkit -i gas.in -o gas.out
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| − | 544 module list
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| − | 545 srun -N 1 -n 40 -t 4:00:00 -p short-40core --pty bash
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| − | 546 rd
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| − | 547 vi ~/.bashrc
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| − | 548 source ~/.bashrc
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| − | 549 rd
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| − | 550 home
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| − | 551 ls
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| − | 552 cd gas_test/
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| − | 554 cd gas_f_test/
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| − | 555 vi diff.out
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| − | 557 cd gas_RD_test
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| − | 559 cd gas_RD_Test/
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| − | 560 ls
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| − | 561 vi diff.out
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| − | 562 history
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| − | 564 vi output_scored.mol2
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| − | 565 cd ..
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| − | 566 cd gas_f_test/
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| − | 567 ls
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| − | 568 vi gas_50.out_scored.mol2
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| − | 569 home
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| − | 570 ls
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| − | 571 cd builds/
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| − | 573 cd ..
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| − | 574 ls
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| − | 575 cd gas_test/gas_f_test/
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| − | 576 ls
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| − | 577 vi gas_50.out_scored.mol2
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| − | 578 awk '{print $9}' gas_50.out_scored.mol2
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| − | 579 :q
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| − | 580 vi gas_50.out_scored.mol2
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| − | 581 awk '{print $9}' gas_50.out_scored.mol2
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| − | 582 :q
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| − | 583 awk '{print $9}' gas_50.out_scored.mol2 > charges.txt
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| − | 584 vi charges.txt
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| − | 585 cd ..
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| − | 586 cd gas_RD_Test/
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| − | 587 ls
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| − | 588 awk '{print $9}' output_scored.mol2 > RD_charges.txt
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| − | 589 vi RD_charges.txt
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| − | 590 ls
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| − | 591 cd ..
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| − | 592 ls
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| − | 593 awk '{print $9}' 4s0v_GA_output.restart0050.mol2 > charges.txt
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| − | 594 vi charges.txt
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| − | 595 mkdir charge_data.txt
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| − | 596 ls
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| − | 597 mv charge_data.txt/ charge_data/
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| − | 598 ls
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| − | 599 mv charges.txt charge_data/
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| − | 600 cd charge_data/
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| − | 601 ls
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| − | 602 mv charges.txt original_charges.txt
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| − | 603 cd ..
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| − | 604 ls
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| − | 605 cd gas_f_test/
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| − | 606 ls
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| − | 607 mv charges.txt f_charges.txt
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| − | 608 cd ..
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| − | 609 mv gas_f_test/f_charges.txt charge_data/
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| − | 610 ls
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| − | 611 ls charge_data/
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| − | 612 ls
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| − | 613 cd gas_RD_Test/
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| − | 614 ls
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| − | 615 cd ..
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| − | 616 mv gas_RD_Test/RD_charges.txt charge_data/
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| − | 617 ls
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| − | 618 exit
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| − | 619 home
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| − | 620 cd gas_test/
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| − | 621 cd charge_data/
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| − | 622 paste -d "," original_charges.txt f_charges.txt RD_charges.txt > gasteiger_charges.csv
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| − | 623 vi gasteiger_charges.csv
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| − | 624 vi original_charges.txt
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| − | 625 cd ..
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| − | 626 vi 4s0v_GA_output.restart0050.mol2
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| − | 627 ls
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| − | 628 cd charge_data/
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| − | 629 ls
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| − | 630 pwd
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| − | 631 exit
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| − | 632 home
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| − | 633 cd ..
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| − | 634 ls
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| − | 635 cd AMS536
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| − | 636 ls
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| − | 637 cd 2025
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| − | 638 ls
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| − | 639 cd additional_files/
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| − | 640 ls
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| − | 641 cd ..
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| − | 642 cd 2025
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| − | 643 pwd
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| − | 644 vi ~/.bashrc
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| − | 645 home
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| − | 646 source ~/.bashrc
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| − | 647 class
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| − | 648 home
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| − | 649 ls
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| − | 650 exit
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| − | 651 home
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| − | 652 ls
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| − | 653 cd 4s0v/
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| − | 654 ls
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| − | 655 cd gas_teiger/
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| − | 656 ls
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| − | 657 cd no_charge/
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| − | 658 ls
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| − | 659 cd ..
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| − | 660 vi no_gas.in
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| − | 661 vi no_gas.out_scored.mol2
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| − | 662 cd ..
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| − | 663 ls
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| − | 664 cd GA_data/
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| − | 665 ls
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| − | 667 cd gas_teiger/
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| − | 668 ls
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| − | 669 vi gas.out_scored.mol2
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| − | 670 exit
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| − | 671 home
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| − | 672 ls
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| − | 673 cd gas_test/
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| − | 674 ls
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| − | 675 cd ..
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| − | 676 ls
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| − | 677 cd 4s0v/
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| − | 678 ls
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| − | 679 cd s
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| − | 680 cd structure/
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| − | 683 ls
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| − | 684 cd ..
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| − | 685 cd gas_test/
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| − | 686 ls
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| − | 687 cd gas_f_test/
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| − | 688 ls
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| − | 689 vi gas_1.in
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| − | 690 cd ..
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| − | 691 ls
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| − | 693 cd 4s0v/gas_teiger/
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| − | 694 ls
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| − | 695 vi gas.in
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| − | 696 module
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| − | 697 module list
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| − | 701 cd structure/
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| − | 704 cd gas_teiger/
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| − | 710 vi gas.out_scored.mol2
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| − | 713 vi gas_teiger/
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| − | 714 cd gas_teiger/
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| − | 716 vi gas.in
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| − | 717 dock6 -i gas.in -o gas.out
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| − | 719 vi gas.out
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| − | 720 vi gas.out_scored.mol2
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| − | 723 cd energy_min/
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| − | 724 ls
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| − | 727 cd 4s0v/
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| − | 728 ls
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| − | 729 vi gas_teiger/
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| − | 730 cd gas_teiger/
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| − | 731 vi gas.
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| − | 732 vi gas.in
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| − | 733 dock6 -i gas.in -o gas.out
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| − | 734 ls
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| − | 737 cd ..
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| − | 738 cd surface_spheres/
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| − | 741 cd gas_test/
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| − | 747 cd surface_spheres/
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| − | 750 ls
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| − | 751 cd gas_teiger/
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| − | 752 ls
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| − | 753 vi gas.in
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| − | 754 dock6 -i gas.in -o gas.out
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| − | 755 ls
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| − | 756 vi gas.out
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| − | 757 vi gas.out_scored.mol2
| |
| − | 758 vi gas.in
| |
| − | 759 dock6 -i gas.in -o gas.out
| |
| − | 760 ls
| |
| − | 761 vi gas.out
| |
| − | 762 vi gas.out_scored.mol2
| |
| − | 763 exit
| |
| − | 764 home
| |
| − | 765 class
| |
| − | 766 ls
| |
| − | 767 cd additional_files/
| |
| − | 768 ls
| |
| − | 769 vi sample_bashrc_4seawulf.txt
| |
| − | 770 exit
| |
| − | 771 home
| |
| − | 772 ls
| |
| − | 773 cd builds/
| |
| − | 774 cd alpha_branch/
| |
| − | 775 ls
| |
| − | 776 cd install/
| |
| − | 777 ls
| |
| − | 778 cd ..
| |
| − | 779 l
| |
| − | 780 ls
| |
| − | 781 cd install/
| |
| − | 782 ls
| |
| − | 783 cd ..
| |
| − | 784 ls
| |
| − | 785 cd bin/
| |
| − | 786 ls
| |
| − | 787 vi dock6.rdkit
| |
| − | 788 cd ..
| |
| − | 789 cd src/
| |
| − | 790 ls
| |
| − | 791 vi Makefile
| |
| − | 792 cd rdkit/
| |
| − | 793 ls
| |
| − | 794 vi Makefile
| |
| − | 795 ls
| |
| − | 796 module list
| |
| − | 797 module load git
| |
| − | 798 module list
| |
| − | 799 git branch
| |
| − | 800 exit
| |
| − | 801 home
| |
| − | 802 ls
| |
| − | 803 cd gas_test/
| |
| − | 804 ls
| |
| − | 805 cd ..
| |
| − | 806 ls
| |
| − | 807 cd 4s0v/
| |
| − | 808 ls
| |
| − | 809 cd structure/
| |
| − | 810 ls
| |
| − | 811 cd ..
| |
| − | 812 cp structure/4s0v_ligand_hydrogens_charges.mol2 gas_teiger/
| |
| − | 813 cd gas_teiger/
| |
| − | 814 ls
| |
| − | 815 vi 4s0v_ligand_hydrogens_charges.mol2
| |
| − | 816 pwd
| |
| − | 817 ls
| |
| − | 818 cd no_charge/
| |
| − | 819 ls
| |
| − | 820 vi gas_2.out
| |
| − | 821 vi gas_2.in
| |
| − | 822 cd ..
| |
| − | 823 mv 4s0v_ligand_hydrogens_charges.mol2 no_charge/
| |
| − | 824 cd no_charge/
| |
| − | 825 ls
| |
| − | 826 vi gas_2.in
| |
| − | 827 dock6 -i gas_2.in -o gas_2.out
| |
| − | 828 vi gas_2.out
| |
| − | 829 vi gas_2.in
| |
| − | 830 dock6 -i gas_2.in -o gas_2.out
| |
| − | 831 ls
| |
| − | 832 vi gas_2.out
| |
| − | 833 vi gas_2.in
| |
| − | 834 dock6 -i gas_2.in -o gas_2.out
| |
| − | 835 ls
| |
| − | 836 vi gas_2.out
| |
| − | 837 mv 4s0v_ligand_hydrogens_charges.mol2 4s0v_ligand_hydrogens_no_charges.mol2
| |
| − | 838 ls
| |
| − | 839 cd ..
| |
| − | 840 cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/no_charge/
| |
| − | 841 ls
| |
| − | 842 cd gas_teiger/no_charge/
| |
| − | 843 ls
| |
| − | 844 vi 4s0v.lig.min_scored.mol2
| |
| − | 845 vimdiff 4s0v.lig.min_scored.mol2 4s0v_ligand_hydrogens_no_charges.mol2
| |
| − | 846 vi 4s0v.lig.min_scored.mol2
| |
| − | 847 mv 4s0v.lig.min_scored.mol2 4s0v.lig_no_charge.min_scored.mol2
| |
| − | 848 vi gas_2.in
| |
| − | 849 dock6 -i gas_2.in -o gas_2.out
| |
| − | 850 ls
| |
| − | 851 vi gas_2.out
| |
| − | 852 vi gas_2.in
| |
| − | 853 vi gas.out_scored.mol2
| |
| − | 854 exit
| |
| − | 855 home
| |
| − | 856 cd 4s0v/
| |
| − | 857 ls
| |
| − | 858 cd gas_teiger/no_charge/
| |
| − | 859 vi gas_2.in
| |
| − | 860 vi 4s0v.lig_no_charge.min_scored.mol2
| |
| − | 861 vi gas_2.out
| |
| − | 862 cd ..
| |
| − | 863 ls
| |
| − | 864 vi gas.in
| |
| − | 865 vi gas.out
| |
| − | 866 exit
| |
| − | 867 home
| |
| − | 868 ls
| |
| − | 869 cd 4s0v/
| |
| − | 870 ls
| |
| − | 871 cd gas_teiger/
| |
| − | 872 ls
| |
| − | 873 vi no_gas.in
| |
| − | 874 vi no_gas.out
| |
| − | 875 vi no_gas.out_scored.mol2
| |
| − | 876 exit
| |
| − | 877 class
| |
| − | 878 pwd
| |
| − | 879 cd ..
| |
| − | 880 vi ~/.bashrc
| |
| − | 881 source ~/.bashrc
| |
| − | 882 home
| |
| − | 883 class
| |
| − | 884 exit
| |
| − | 885 class
| |
| − | 886 mkdir ehspector
| |
| − | 887 ls
| |
| − | 888 cd ehspector/
| |
| − | 889 ls
| |
| − | 890 touch file.txt
| |
| − | 891 ls
| |
| − | 892 cd ..
| |
| − | 893 cd
| |
| − | 894 ls
| |
| − | 895 mkdir class_project
| |
| − | 896 ls
| |
| − | 897 exit
| |
| − | 898 home
| |
| − | 899 ls
| |
| − | 900 cd builds/
| |
| − | 901 ls
| |
| − | 902 cd alpha_branch/
| |
| − | 903 ls
| |
| − | 904 module load git
| |
| − | 905 git branch
| |
| − | 906 git config --get remote.origin.url
| |
| − | 907 git pull
| |
| − | 908 git status
| |
| − | 909 git diff src/dock/dock.cpp
| |
| − | 910 git diff src/dock/gasteiger.cpp
| |
| − | 911 git diff src/dock/orient.cpp
| |
| − | 912 git diff src/dock/sphere.cpp
| |
| − | 913 ls
| |
| − | 914 cd src/dock
| |
| − | 915 vi gasteiger.cpp
| |
| − | 916 git diff gasteiger.cpp
| |
| − | 917 vi gasteiger.cpp
| |
| − | 918 git diff gasteiger.cpp
| |
| − | 919 git status gasteiger.cpp
| |
| − | 920 vi gasteiger.cpp
| |
| − | 921 git diff gasteiger.cpp
| |
| − | 922 git status gasteiger.cpp
| |
| − | 923 git status
| |
| − | 924 git diff sphere.cpp
| |
| − | 925 exit
| |
| − | 926 home
| |
| − | 927 class
| |
| − | 928 cd
| |
| − | 929 ls
| |
| − | 930 mv class_project/ AMS_536
| |
| − | 931 ls
| |
| − | 932 cd AMS_536/
| |
| − | 933 ls
| |
| − | 934 mkdir class_work
| |
| − | 935 mkdir class_project
| |
| − | 936 cd ..
| |
| − | 937 cd AMS_536/
| |
| − | 938 pwd
| |
| − | 939 vi ~/.bashrc
| |
| − | 940 source ~/.bashrc
| |
| − | 941 home
| |
| − | 942 class
| |
| − | 943 ls
| |
| − | 944 pwd
| |
| − | 945 cd ..
| |
| − | 946 cd projects/
| |
| − | 947 ls
| |
| − | 948 cd AMS536
| |
| − | 949 cd zzz.programs
| |
| − | 950 ls
| |
| − | 951 cd dock6.12_ams536/
| |
| − | 952 ls
| |
| − | 953 cd bin/
| |
| − | 954 ls
| |
| − | 955 cd
| |
| − | 956 man date
| |
| − | 957 ls
| |
| − | 958 cd ..
| |
| − | 959 cd projects/AMS536/
| |
| − | 960 ls
| |
| − | 961 cd 2025/
| |
| − | 962 ls
| |
| − | 963 cd rotations/
| |
| − | 964 ls
| |
| − | 965 cd ..
| |
| − | 966 ls
| |
| − | 967 cd 2025/
| |
| − | 968 ls
| |
| − | 969 cd additional_files/
| |
| − | 970 ls
| |
| − | 971 cd ..
| |
| − | 972 ls
| |
| − | 973 cd ..
| |
| − | 974 ls
| |
| − | 975 vi junk.txt
| |
| − | 976 ls
| |
| − | 977 cd 2025
| |
| − | 978 ls
| |
| − | 979 cd
| |
| − | 980 cd ../../
| |
| − | 981 sinfo
| |
| − | 982 alias
| |
| − | 983 class
| |
| − | 984 ls
| |
| − | 985 cd class_work/
| |
| − | 986 ls
| |
| − | 987 touch Notes.txt
| |
| − | 988 vi Notes.txt
| |
| − | 989 class
| |
| − | 990 cd ..
| |
| − | 991 class
| |
| − | 992 ls
| |
| − | 993 cd class_work/
| |
| − | 994 ls
| |
| − | 995 vi Notes.txt
| |
| − | 996 which dock6
| |
| − | 997 vi Notes.txt
| |
| − | 998 vi ~/.bashrc
| |
| − | 999 exit
| |
| − | 1000 home
| |
| − | 1001 module list
| |
| − | 1002 module load git
| |
| − | 1003 git diff
| |
| − | 1004 git status
| |
| − | 1005 git branch
| |
| − | 1006 ls
| |
| − | 1007 module list
| |
| − | 1008 history
| |
| − | (base) [ehspector@login1 espector]$ git branch
| |
| − | fatal: not a git repository (or any parent up to mount point /)
| |
| − | Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
| |
| − | (base) [ehspector@login1 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login1 espector]$ cd builds/alpha_branch/
| |
| − | (base) [ehspector@login1 alpha_branch]$ git branch
| |
| − | * alpha_branch
| |
| − | master
| |
| − | (base) [ehspector@login1 alpha_branch]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
| |
| − | (use "git pull" to update your local branch)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add/rm <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | deleted: install/test/minimization/minimize7.dockout
| |
| − | modified: src/dock/dock.cpp
| |
| − | modified: src/dock/filter.cpp
| |
| − | modified: src/dock/filter.h
| |
| − | modified: src/dock/orient.cpp
| |
| − | modified: src/dock/sphere.cpp
| |
| − | modified: src/rdkit/Makefile
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | src/dock/lol
| |
| − | src/rdkit/boost/
| |
| − | src/rdkit/boost_1_71_0.tar.gz
| |
| − | src/rdkit/boost_1_71_0/
| |
| − | src/rdkit/eigen-3.3.9.tar.gz
| |
| − | src/rdkit/eigen-3.3.9/
| |
| − | src/rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | src/rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@login1 alpha_branch]$ cd src/dock
| |
| − | (base) [ehspector@login1 dock]$ ;s
| |
| − | -bash: syntax error near unexpected token `;'
| |
| − | (base) [ehspector@login1 dock]$ ls
| |
| − | amber_typer.cpp filter.o mem_info.h score_internal.cpp
| |
| − | amber_typer.h fingerprint.cpp mem_info.o score_internal.h
| |
| − | amber_typer.o fingerprint.h nab score_internal.o
| |
| − | base_grid.cpp fingerprint.o nabcode.h score_multigrid.cpp
| |
| − | base_grid.h fraggraph.cpp nab.h score_multigrid.h
| |
| − | base_grid.o fraggraph.h orient.cpp score_multigrid.o
| |
| − | base_mpi.cpp fraggraph.o orient.h score.o
| |
| − | base_mpi.h fragment.cpp orient.o score_ph4.cpp
| |
| − | base_mpi.o fragment.h rddrive.cpp score_ph4.h
| |
| − | base_score.cpp fragment.o rddrive.h score_ph4.o
| |
| − | base_score.h gasteiger.cpp rddrive.o score_sasa.cpp
| |
| − | base_score.o gasteiger.h rdtyper.cpp score_sasa.h
| |
| − | conf_gen_ag.cpp gasteiger.o rdtyper.h score_sasa.o
| |
| − | conf_gen_ag.h grid.cpp rdtyper.o score_solvent.cpp
| |
| − | conf_gen_ag.o grid.h README score_solvent.h
| |
| − | conf_gen_cg.cpp grid.o sasa.cpp score_solvent.o
| |
| − | conf_gen_cg.h gzstream sasa.h score_volume.cpp
| |
| − | conf_gen_cg.o hungarian.cpp sasa.o score_volume.h
| |
| − | conf_gen_dn.cpp hungarian.h score_amber.cpp score_volume.o
| |
| − | conf_gen_dn_ga.cpp hungarian.o score_amber.h simplex.cpp
| |
| − | conf_gen_dn_ga.h iso_align.cpp score_amber.o simplex.h
| |
| − | conf_gen_dn_ga.o iso_align.h score_chemgrid.cpp simplex.o
| |
| − | conf_gen_dn.h iso_align.o score_chemgrid.h sphere.cpp
| |
| − | conf_gen_dn.o library_file.cpp score_chemgrid.o sphere.h
| |
| − | conf_gen_ga.cpp library_file.h score.cpp sphere.o
| |
| − | conf_gen_ga.h library_file.o score_descriptor.cpp tnt
| |
| − | conf_gen_ga.o limit_max_change.cpp score_descriptor.h trace.cpp
| |
| − | conf_gen_hdb.cpp limit_max_change.h score_descriptor.o trace.h
| |
| − | conf_gen_hdb.h limit_max_change.o score_footprint.cpp trace.inl
| |
| − | conf_gen_hdb.o lol score_footprint.h trace.o
| |
| − | defreal.h Makefile score_footprint.o utils.cpp
| |
| − | dock.cpp master_conf.cpp score_gist.cpp utils.h
| |
| − | dockmol.cpp master_conf.h score_gist.h utils.o
| |
| − | dockmol.h master_conf.o score_gist.o version.h
| |
| − | dockmol.o master_score.cpp score.h xlogp.cpp
| |
| − | dock.o master_score.h score_hbond.cpp xlogp.h
| |
| − | filter.cpp master_score.o score_hbond.h
| |
| − | filter.h mem_info.cpp score_hbond.o
| |
| − | (base) [ehspector@login1 dock]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
| |
| − | (use "git pull" to update your local branch)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add/rm <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | deleted: ../../install/test/minimization/minimize7.dockout
| |
| − | modified: dock.cpp
| |
| − | modified: filter.cpp
| |
| − | modified: filter.h
| |
| − | modified: orient.cpp
| |
| − | modified: sphere.cpp
| |
| − | modified: ../rdkit/Makefile
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | lol
| |
| − | ../rdkit/boost/
| |
| − | ../rdkit/boost_1_71_0.tar.gz
| |
| − | ../rdkit/boost_1_71_0/
| |
| − | ../rdkit/eigen-3.3.9.tar.gz
| |
| − | ../rdkit/eigen-3.3.9/
| |
| − | ../rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | ../rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@login1 dock]$ git diff dock.cpp
| |
| − | diff --git a/src/dock/dock.cpp b/src/dock/dock.cpp
| |
| − | index 81925eac..e447b601 100644
| |
| − | --- a/src/dock/dock.cpp
| |
| − | +++ b/src/dock/dock.cpp
| |
| − | @@ -820,7 +820,7 @@ main(int argc, char **argv)
| |
| − | if (c_filter.use_database_filter)
| |
| − | {
| |
| − | //calculate RDKIT-related descriptors for the ligand
| |
| − | - c_filter.calc_descriptors(mol);
| |
| − | + c_filter.calc_descriptors(mol, c_typer);
| |
| − | //other descriptors are now computed & printed in amber_typer.cpp
| |
| − | //print out the descriptors
| |
| − | //cout << c_filter.get_descriptors(mol);
| |
| − | (base) [ehspector@login1 dock]$ git diff orient.cpp
| |
| − | diff --git a/src/dock/orient.cpp b/src/dock/orient.cpp
| |
| − | index 92d58f71..2d63fece 100644
| |
| − | --- a/src/dock/orient.cpp
| |
| − | +++ b/src/dock/orient.cpp
| |
| − | @@ -461,8 +461,7 @@ Orient::get_spheres()
| |
| − | spheres = Active_Site_Spheres :: get_instance();
| |
| − | num_spheres = spheres.size();
| |
| − |
| |
| − | - if (verbose) cout << "Read in " << num_spheres
| |
| − | - << " spheres for orienting." << endl;
| |
| − | + cout << "Read in " << num_spheres << " spheres for orienting." << endl;
| |
| − |
| |
| − | // process critical points
| |
| − | if (critical_points) {
| |
| − | (base) [ehspector@login1 dock]$ vi orient.cpp
| |
| − | (base) [ehspector@login1 dock]$ vi orient.cpp
| |
| − | (base) [ehspector@login1 dock]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
| |
| − | (use "git pull" to update your local branch)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add/rm <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | deleted: ../../install/test/minimization/minimize7.dockout
| |
| − | modified: dock.cpp
| |
| − | modified: filter.cpp
| |
| − | modified: filter.h
| |
| − | modified: orient.cpp
| |
| − | modified: sphere.cpp
| |
| − | modified: ../rdkit/Makefile
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | lol
| |
| − | ../rdkit/boost/
| |
| − | ../rdkit/boost_1_71_0.tar.gz
| |
| − | ../rdkit/boost_1_71_0/
| |
| − | ../rdkit/eigen-3.3.9.tar.gz
| |
| − | ../rdkit/eigen-3.3.9/
| |
| − | ../rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | ../rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@login1 dock]$ cd ..
| |
| − | (base) [ehspector@login1 src]$ cd rdkit
| |
| − | (base) [ehspector@login1 rdkit]$ vi Makefile
| |
| − | (base) [ehspector@login1 rdkit]$ cd ..
| |
| − | (base) [ehspector@login1 src]$ cd dock
| |
| − | (base) [ehspector@login1 dock]$ git diff orient.cpp
| |
| − | diff --git a/src/dock/orient.cpp b/src/dock/orient.cpp
| |
| − | index 92d58f71..ff8d8a36 100644
| |
| − | --- a/src/dock/orient.cpp
| |
| − | +++ b/src/dock/orient.cpp
| |
| − | @@ -460,9 +460,9 @@ Orient::get_spheres()
| |
| − |
| |
| − | spheres = Active_Site_Spheres :: get_instance();
| |
| − | num_spheres = spheres.size();
| |
| − | -
| |
| − | - if (verbose) cout << "Read in " << num_spheres
| |
| − | - << " spheres for orienting." << endl;
| |
| − | +
| |
| − | + // prints the number of spheres that are generated EHS 9/18/23
| |
| − | + cout << "Read in " << num_spheres << " spheres for orienting." << endl;
| |
| − |
| |
| − | // process critical points
| |
| − | if (critical_points) {
| |
| − | (base) [ehspector@login1 dock]$ git diff sphere.cpp
| |
| − | diff --git a/src/dock/sphere.cpp b/src/dock/sphere.cpp
| |
| − | index 27641d83..5739a67c 100644
| |
| − | --- a/src/dock/sphere.cpp
| |
| − | +++ b/src/dock/sphere.cpp
| |
| − | @@ -111,6 +111,7 @@ read_spheres( string sphere_file_name, SphereVec & spheres )
| |
| − | fclose(sphere_file);
| |
| − |
| |
| − | return num_spheres;
| |
| − | +
| |
| − | }
| |
| − |
| |
| − |
| |
| − | (base) [ehspector@login1 dock]$ vi sphere.cpp
| |
| − | (base) [ehspector@login1 dock]$ ls
| |
| − | amber_typer.cpp filter.o mem_info.h score_internal.cpp
| |
| − | amber_typer.h fingerprint.cpp mem_info.o score_internal.h
| |
| − | amber_typer.o fingerprint.h nab score_internal.o
| |
| − | base_grid.cpp fingerprint.o nabcode.h score_multigrid.cpp
| |
| − | base_grid.h fraggraph.cpp nab.h score_multigrid.h
| |
| − | base_grid.o fraggraph.h orient.cpp score_multigrid.o
| |
| − | base_mpi.cpp fraggraph.o orient.h score.o
| |
| − | base_mpi.h fragment.cpp orient.o score_ph4.cpp
| |
| − | base_mpi.o fragment.h rddrive.cpp score_ph4.h
| |
| − | base_score.cpp fragment.o rddrive.h score_ph4.o
| |
| − | base_score.h gasteiger.cpp rddrive.o score_sasa.cpp
| |
| − | base_score.o gasteiger.h rdtyper.cpp score_sasa.h
| |
| − | conf_gen_ag.cpp gasteiger.o rdtyper.h score_sasa.o
| |
| − | conf_gen_ag.h grid.cpp rdtyper.o score_solvent.cpp
| |
| − | conf_gen_ag.o grid.h README score_solvent.h
| |
| − | conf_gen_cg.cpp grid.o sasa.cpp score_solvent.o
| |
| − | conf_gen_cg.h gzstream sasa.h score_volume.cpp
| |
| − | conf_gen_cg.o hungarian.cpp sasa.o score_volume.h
| |
| − | conf_gen_dn.cpp hungarian.h score_amber.cpp score_volume.o
| |
| − | conf_gen_dn_ga.cpp hungarian.o score_amber.h simplex.cpp
| |
| − | conf_gen_dn_ga.h iso_align.cpp score_amber.o simplex.h
| |
| − | conf_gen_dn_ga.o iso_align.h score_chemgrid.cpp simplex.o
| |
| − | conf_gen_dn.h iso_align.o score_chemgrid.h sphere.cpp
| |
| − | conf_gen_dn.o library_file.cpp score_chemgrid.o sphere.h
| |
| − | conf_gen_ga.cpp library_file.h score.cpp sphere.o
| |
| − | conf_gen_ga.h library_file.o score_descriptor.cpp tnt
| |
| − | conf_gen_ga.o limit_max_change.cpp score_descriptor.h trace.cpp
| |
| − | conf_gen_hdb.cpp limit_max_change.h score_descriptor.o trace.h
| |
| − | conf_gen_hdb.h limit_max_change.o score_footprint.cpp trace.inl
| |
| − | conf_gen_hdb.o lol score_footprint.h trace.o
| |
| − | defreal.h Makefile score_footprint.o utils.cpp
| |
| − | dock.cpp master_conf.cpp score_gist.cpp utils.h
| |
| − | dockmol.cpp master_conf.h score_gist.h utils.o
| |
| − | dockmol.h master_conf.o score_gist.o version.h
| |
| − | dockmol.o master_score.cpp score.h xlogp.cpp
| |
| − | dock.o master_score.h score_hbond.cpp xlogp.h
| |
| − | filter.cpp master_score.o score_hbond.h
| |
| − | filter.h mem_info.cpp score_hbond.o
| |
| − | (base) [ehspector@login1 dock]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
| |
| − | (use "git pull" to update your local branch)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add/rm <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | deleted: ../../install/test/minimization/minimize7.dockout
| |
| − | modified: dock.cpp
| |
| − | modified: filter.cpp
| |
| − | modified: filter.h
| |
| − | modified: orient.cpp
| |
| − | modified: ../rdkit/Makefile
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | lol
| |
| − | ../rdkit/boost/
| |
| − | ../rdkit/boost_1_71_0.tar.gz
| |
| − | ../rdkit/boost_1_71_0/
| |
| − | ../rdkit/eigen-3.3.9.tar.gz
| |
| − | ../rdkit/eigen-3.3.9/
| |
| − | ../rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | ../rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@login1 dock]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % pip install pandas --upgrade
| |
| − | Requirement already satisfied: pandas in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (2.0.3)
| |
| − | Collecting pandas
| |
| − | Obtaining dependency information for pandas from https://files.pythonhosted.org/packages/a8/44/d9502bf0ed197ba9bf1103c9867d5904ddcaf869e52329787fc54ed70cc8/pandas-2.2.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata
| |
| − | Downloading pandas-2.2.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata (89 kB)
| |
| − | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.9/89.9 kB 1.2 MB/s eta 0:00:00
| |
| − | Requirement already satisfied: numpy>=1.23.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (1.26.4)
| |
| − | Requirement already satisfied: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (2.8.2)
| |
| − | Requirement already satisfied: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (2023.3.post1)
| |
| − | Requirement already satisfied: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas) (2023.3)
| |
| − | Requirement already satisfied: six>=1.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas) (1.16.0)
| |
| − | Downloading pandas-2.2.3-cp311-cp311-macosx_10_9_x86_64.whl (12.6 MB)
| |
| − | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.6/12.6 MB 18.7 MB/s eta 0:00:00
| |
| − | Installing collected packages: pandas
| |
| − | Attempting uninstall: pandas
| |
| − | Found existing installation: pandas 2.0.3
| |
| − | Uninstalling pandas-2.0.3:
| |
| − | Successfully uninstalled pandas-2.0.3
| |
| − | Successfully installed pandas-2.2.3
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % polaris login
| |
| − | /Users/supremestudier/anaconda3/lib/python3.11/site-packages/pandas/core/arrays/masked.py:60: UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.5' currently installed).
| |
| − | from pandas.core import (
| |
| − | [2025-02-02 22:02:58] INFO You are successfully logged in to the Polaris client.py:252
| |
| − | Hub.
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % python --version
| |
| − | Python 3.11.5
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % pip install fsspec==2024.12.0
| |
| − | Collecting fsspec==2024.12.0
| |
| − | Obtaining dependency information for fsspec==2024.12.0 from https://files.pythonhosted.org/packages/de/86/5486b0188d08aa643e127774a99bac51ffa6cf343e3deb0583956dca5b22/fsspec-2024.12.0-py3-none-any.whl.metadata
| |
| − | Downloading fsspec-2024.12.0-py3-none-any.whl.metadata (11 kB)
| |
| − | Downloading fsspec-2024.12.0-py3-none-any.whl (183 kB)
| |
| − | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 183.9/183.9 kB 2.5 MB/s eta 0:00:00
| |
| − | Installing collected packages: fsspec
| |
| − | Attempting uninstall: fsspec
| |
| − | Found existing installation: fsspec 2023.4.0
| |
| − | Uninstalling fsspec-2023.4.0:
| |
| − | Successfully uninstalled fsspec-2023.4.0
| |
| − | ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
| |
| − | s3fs 2023.4.0 requires fsspec==2023.4.0, but you have fsspec 2024.12.0 which is incompatible.
| |
| − | Successfully installed fsspec-2024.12.0
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % conda activate
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % ls
| |
| − | Materials Week_2
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % conda environment
| |
| − | usage: conda [-h] [--no-plugins] [-V] COMMAND ...
| |
| − | conda: error: argument COMMAND: invalid choice: 'environment' (choose from 'clean', 'compare', 'config', 'create', 'info', 'init', 'install', 'list', 'notices', 'package', 'remove', 'uninstall', 'rename', 'run', 'search', 'update', 'upgrade', 'build', 'content-trust', 'convert', 'debug', 'develop', 'doctor', 'index', 'inspect', 'metapackage', 'render', 'skeleton', 'env', 'token', 'pack', 'repo', 'server', 'verify')
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % conda install fsspec==2024.12.0
| |
| − | Retrieving notices: ...working... done
| |
| − | Collecting package metadata (current_repodata.json): | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
| |
| − | done
| |
| − | Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
| |
| − | Solving environment: done
| |
| − |
| |
| − |
| |
| − | ==> WARNING: A newer version of conda exists. <==
| |
| − | current version: 23.7.4
| |
| − | latest version: 25.1.1
| |
| − |
| |
| − | Please update conda by running
| |
| − |
| |
| − | $ conda update -n base -c defaults conda
| |
| − |
| |
| − | Or to minimize the number of packages updated during conda update use
| |
| − |
| |
| − | conda install conda=25.1.1
| |
| − |
| |
| − |
| |
| − | Collecting package metadata (repodata.json): | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
| |
| − | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
| |
| − | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0
| |
| − | done
| |
| − | Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
| |
| − | Solving environment: - failed
| |
| − |
| |
| − | CondaError: KeyboardInterrupt
| |
| − |
| |
| − | (base) supremestudier@Evans-MBP AMS_500 % cd ..
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % pip show fsspec
| |
| − | Name: fsspec
| |
| − | Version: 2024.12.0
| |
| − | Summary: File-system specification
| |
| − | Home-page:
| |
| − | Author:
| |
| − | Author-email:
| |
| − | License: BSD 3-Clause License
| |
| − |
| |
| − | Copyright (c) 2018, Martin Durant
| |
| − | All rights reserved.
| |
| − |
| |
| − | Redistribution and use in source and binary forms, with or without
| |
| − | modification, are permitted provided that the following conditions are met:
| |
| − |
| |
| − | * Redistributions of source code must retain the above copyright notice, this
| |
| − | list of conditions and the following disclaimer.
| |
| − |
| |
| − | * Redistributions in binary form must reproduce the above copyright notice,
| |
| − | this list of conditions and the following disclaimer in the documentation
| |
| − | and/or other materials provided with the distribution.
| |
| − |
| |
| − | * Neither the name of the copyright holder nor the names of its
| |
| − | contributors may be used to endorse or promote products derived from
| |
| − | this software without specific prior written permission.
| |
| − |
| |
| − | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
| |
| − | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
| |
| − | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
| |
| − | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
| |
| − | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
| |
| − | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
| |
| − | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
| |
| − | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
| |
| − | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
| |
| − | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
| |
| − | Location: /Users/supremestudier/anaconda3/lib/python3.11/site-packages
| |
| − | Requires:
| |
| − | Required-by: dask, datamol, datasets, huggingface-hub, intake, polaris-lib, s3fs
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % polaris login
| |
| − | /Users/supremestudier/anaconda3/lib/python3.11/site-packages/pandas/core/arrays/masked.py:60: UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.5' currently installed).
| |
| − | from pandas.core import (
| |
| − | [2025-02-03 15:53:30] INFO You are successfully logged in to the Polaris client.py:252
| |
| − | Hub.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % pip install pymol
| |
| − | ERROR: Could not find a version that satisfies the requirement pymol (from versions: none)
| |
| − | ERROR: No matching distribution found for pymol
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % conda activate
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % conda install -c schrodinger pymol
| |
| − | Collecting package metadata (current_repodata.json): | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
| |
| − | done
| |
| − | Solving environment: - unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
| |
| − |
| |
| − | CondaError: KeyboardInterrupt
| |
| − |
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Permission denied, please try again.
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login1 ~]$ ls
| |
| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@login1 ~]$ cd AMS_536/
| |
| − | (base) [ehspector@login1 AMS_536]$ ls
| |
| − | class_project class_work
| |
| − | (base) [ehspector@login1 AMS_536]$ cd class_work/
| |
| − | (base) [ehspector@login1 class_work]$ ls
| |
| − | Notes.txt
| |
| − | (base) [ehspector@login1 class_work]$ vi Notes.txt
| |
| − | (base) [ehspector@login1 class_work]$ touch commands.txt
| |
| − | (base) [ehspector@login1 class_work]$ vi commands.txt
| |
| − | (base) [ehspector@login1 class_work]$ bash commands.txt
| |
| − | (base) [ehspector@login1 class_work]$ ls
| |
| − | 001_structure commands.txt Notes.txt
| |
| − | (base) [ehspector@login1 class_work]$ vi commands.txt
| |
| − | (base) [ehspector@login1 class_work]$ bash commands.txt
| |
| − | mkdir: cannot create directory ‘001_structure’: File exists
| |
| − | (base) [ehspector@login1 class_work]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@login1 class_work]$ exit
| |
| − | logout
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login1 ~]$ class
| |
| − | (base) [ehspector@login1 AMS_536]$ ls
| |
| − | class_project class_work
| |
| − | (base) [ehspector@login1 AMS_536]$ cd class_work/
| |
| − | (base) [ehspector@login1 class_work]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@login1 class_work]$ cd 001_structure/
| |
| − | (base) [ehspector@login1 001_structure]$ pwd
| |
| − | /gpfs/home/ehspector/AMS_536/class_work/001_structure
| |
| − | (base) [ehspector@login1 001_structure]$ ^C
| |
| − | (base) [ehspector@login1 001_structure]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login1 ~]$ exit
| |
| − | logout
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login1 ~]$ class
| |
| − | (base) [ehspector@login1 AMS_536]$ cd class_work/
| |
| − | (base) [ehspector@login1 class_work]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@login1 class_work]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@login1 002_surface_spheres]$ ls
| |
| − | 2w26_surface.dms
| |
| − | (base) [ehspector@login1 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@login1 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@login1 002_surface_spheres]$ sphgen -i INSPH -o OUTSPH
| |
| − | bash: sphgen: command not found...
| |
| − | (base) [ehspector@login1 002_surface_spheres]$ which sphgen
| |
| − | /usr/bin/which: no sphgen in (/gpfs/home/ehspector/miniconda3/bin:/gpfs/home/ehspector/miniconda3/condabin:/gpfs/software/mvapich/haswell/gcc13.2/2.3.7/bin:/gpfs/software/gcc/haswell/13.2.0/bin:/cm/shared/apps/slurm/17.11.12/sbin:/cm/shared/apps/slurm/17.11.12/bin:/cm/local/apps/environment-modules/4.0.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/4.0.0/bin:/gpfs/software/local/bin:/gpfs/projects/rizzo/espector/builds/alpha_branch/bin:/gpfs/home/ehspector/bin)
| |
| − | (base) [ehspector@login1 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@login1 class_work]$ cd ..
| |
| − | (base) [ehspector@login1 AMS_536]$ cd ..
| |
| − | (base) [ehspector@login1 ~]$ cd ..
| |
| − | (base) [ehspector@login1 home]$ cd ..
| |
| − | (base) [ehspector@login1 gpfs]$ cd projects/AMS536
| |
| − | (base) [ehspector@login1 AMS536]$ ls
| |
| − | 2017 2019 2021 2023 2025 junk.txt zzz.programs
| |
| − | 2018 2020 2022 2024 get_anchors.py zzz.anchors
| |
| − | (base) [ehspector@login1 AMS536]$ cd 2025/
| |
| − | (base) [ehspector@login1 2025]$ ls
| |
| − | additional_files robbashrc_file rotations wed_humpday.txt
| |
| − | (base) [ehspector@login1 2025]$ cd ..
| |
| − | (base) [ehspector@login1 AMS536]$ cd zzz.programs/
| |
| − | (base) [ehspector@login1 zzz.programs]$ ls
| |
| − | amber16 dock6.11 dock6-master.zip plot_footprint_single_magnitude.py
| |
| − | de_novo_anchors dock6.11_alpha dock_directory_arch plot_rmsds_amber
| |
| − | dock6.10 dock6.12 gen-frags-12 VS_libraries
| |
| − | dock6.10_milan dock6.12_ams536 old
| |
| − | (base) [ehspector@login1 zzz.programs]$ cd dock6.12_ams536
| |
| − | (base) [ehspector@login1 dock6.12_ams536]$ ls
| |
| − | bin developer docs install parameters README README.md src template_pipeline tutorials
| |
| − | (base) [ehspector@login1 dock6.12_ams536]$ cd bin/
| |
| − | (base) [ehspector@login1 bin]$ ls
| |
| − | am1bcc combine_torenv.py mol2bild.py parmchk showsphere
| |
| − | amberize_complex dock6 mol2.py prepare_amber.pl solvgrid
| |
| − | amberize_ligand dock6.mpi mopac prepare_rna_amber.pl solvmap
| |
| − | amberize_receptor espgen mopac.sh prepgen sphere_selector
| |
| − | antechamber grid multigrid_fp_gen.py resp sphgen
| |
| − | atomtype grid-convert nchemgrid_GB respgen teLeap
| |
| − | bondtype grid-convrds nchemgrid_SA sevsolv tleap
| |
| − | chemgrid make_phimap parmcal showbox
| |
| − | (base) [ehspector@login1 bin]$ pwd
| |
| − | /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
| |
| − | (base) [ehspector@login1 bin]$ class
| |
| − | (base) [ehspector@login1 AMS_536]$ cd class_work/
| |
| − | (base) [ehspector@login1 class_work]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@login1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH
| |
| − | /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen)
| |
| − | /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
| |
| − | /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libm.so.6: version `GLIBC_2.26' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
| |
| − | /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.26' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
| |
| − | /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /gpfs/software/gcc/13.2.0/lib64/libgfortran.so.5)
| |
| − | (base) [ehspector@login1 002_surface_spheres]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd class_work/
| |
| − | (base) [ehspector@milan1 class_work]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan1 class_work]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 2w26_surface.dms INSPH
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH
| |
| − | At line 328 of file sphgen.f
| |
| − | Fortran runtime error: Bad value during floating point read
| |
| − |
| |
| − | Error termination. Backtrace:
| |
| − | #0 0x7ffff7d59e39 in formatted_transfer_scalar_read
| |
| − | at ../../../libgfortran/io/transfer.c:1790
| |
| − | #1 0x7ffff7d5b535 in formatted_transfer
| |
| − | at ../../../libgfortran/io/transfer.c:2491
| |
| − | #2 0x4049e0 in ???
| |
| − | #3 0x40516a in ???
| |
| − | #4 0x40117c in ???
| |
| − | #5 0x7ffff742958f in ???
| |
| − | #6 0x7ffff742963f in ???
| |
| − | #7 0x4011b4 in ???
| |
| − | #8 0xffffffffffffffff in ???
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 2w26_surface.dms INSPH OUTSPH temp1.ms temp3.atc
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ rm 2w26_surface.dms
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ rm temp1.ms temp3.atc
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | INSPH OUTSPH
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ rm OUTSPH
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd class_work
| |
| − | (base) [ehspector@milan1 class_work]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 2w26_new_surface.dms INSPH
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphgen -i INSPH -o OUTSPH
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 2w26_new_surface.dms 2w26.sph INSPH OUTSPH
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ vi OUTSPH
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Permission denied, please try again.
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ module load git
| |
| − | (base) [ehspector@milan2 ~]$ home
| |
| − | (base) [ehspector@milan2 espector]$ cd builds/
| |
| − | (base) [ehspector@milan2 builds]$ cd alpha_branch/
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git branch
| |
| − | * alpha_branch
| |
| − | master
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git pull
| |
| − | /gpfs/software/git/2.36.2/libexec/git-core/git-remote-https: error while loading shared libraries: libssl.so.10: cannot open shared object file: No such file or directory
| |
| − | (base) [ehspector@milan2 alpha_branch]$ module list
| |
| − | Currently Loaded Modulefiles:
| |
| − | 1) slurm/seawulf3/21.08.8 3) gcc/13.2.0 5) gcc-stack
| |
| − | 2) shared 4) mvapich2/gcc13.2/2.3.7 6) git/2.36.2
| |
| − | (base) [ehspector@milan2 alpha_branch]$ module unload git
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git pull
| |
| − | Username for 'https://github.com': EvanS-Dock6
| |
| − | Password for 'https://EvanS-Dock6@github.com':
| |
| − | Updating 4be5c842..2ce698b4
| |
| − | error: Your local changes to the following files would be overwritten by merge:
| |
| − | src/dock/dock.cpp
| |
| − | src/dock/orient.cpp
| |
| − | Please commit your changes or stash them before you merge.
| |
| − | Aborting
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch is behind 'origin/alpha_branch' by 267 commits, and can be fast-forwarded.
| |
| − | (use "git pull" to update your local branch)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add/rm <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | deleted: install/test/minimization/minimize7.dockout
| |
| − | modified: src/dock/dock.cpp
| |
| − | modified: src/dock/filter.cpp
| |
| − | modified: src/dock/filter.h
| |
| − | modified: src/dock/orient.cpp
| |
| − | modified: src/rdkit/Makefile
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | src/dock/lol
| |
| − | src/rdkit/boost/
| |
| − | src/rdkit/boost_1_71_0.tar.gz
| |
| − | src/rdkit/boost_1_71_0/
| |
| − | src/rdkit/eigen-3.3.9.tar.gz
| |
| − | src/rdkit/eigen-3.3.9/
| |
| − | src/rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | src/rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git add
| |
| − | Nothing specified, nothing added.
| |
| − | hint: Maybe you wanted to say 'git add .'?
| |
| − | hint: Turn this message off by running
| |
| − | hint: "git config advice.addEmptyPathspec false"
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git add src/dock/dock.cpp src/dock/filter.cpp src/dock/filter.h
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git commit -m "feat: ability to gasterize mols"
| |
| − | [alpha_branch 8c38cd54] feat: ability to gasterize mols
| |
| − | 3 files changed, 70 insertions(+), 8 deletions(-)
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch and 'origin/alpha_branch' have diverged,
| |
| − | and have 1 and 267 different commits each, respectively.
| |
| − | (use "git pull" if you want to integrate the remote branch with yours)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add/rm <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | deleted: install/test/minimization/minimize7.dockout
| |
| − | modified: src/dock/orient.cpp
| |
| − | modified: src/rdkit/Makefile
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | src/dock/lol
| |
| − | src/rdkit/boost/
| |
| − | src/rdkit/boost_1_71_0.tar.gz
| |
| − | src/rdkit/boost_1_71_0/
| |
| − | src/rdkit/eigen-3.3.9.tar.gz
| |
| − | src/rdkit/eigen-3.3.9/
| |
| − | src/rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | src/rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git pull
| |
| − | Username for 'https://github.com': EvanS-Dock6
| |
| − | Password for 'https://EvanS-Dock6@github.com':
| |
| − | hint: You have divergent branches and need to specify how to reconcile them.
| |
| − | hint: You can do so by running one of the following commands sometime before
| |
| − | hint: your next pull:
| |
| − | hint:
| |
| − | hint: git config pull.rebase false # merge
| |
| − | hint: git config pull.rebase true # rebase
| |
| − | hint: git config pull.ff only # fast-forward only
| |
| − | hint:
| |
| − | hint: You can replace "git config" with "git config --global" to set a default
| |
| − | hint: preference for all repositories. You can also pass --rebase, --no-rebase,
| |
| − | hint: or --ff-only on the command line to override the configured default per
| |
| − | hint: invocation.
| |
| − | fatal: Need to specify how to reconcile divergent branches.
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git pull --rebase
| |
| − | error: cannot pull with rebase: You have unstaged changes.
| |
| − | error: Please commit or stash them.
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch and 'origin/alpha_branch' have diverged,
| |
| − | and have 1 and 267 different commits each, respectively.
| |
| − | (use "git pull" if you want to integrate the remote branch with yours)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add/rm <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | deleted: install/test/minimization/minimize7.dockout
| |
| − | modified: src/dock/orient.cpp
| |
| − | modified: src/rdkit/Makefile
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | src/dock/lol
| |
| − | src/rdkit/boost/
| |
| − | src/rdkit/boost_1_71_0.tar.gz
| |
| − | src/rdkit/boost_1_71_0/
| |
| − | src/rdkit/eigen-3.3.9.tar.gz
| |
| − | src/rdkit/eigen-3.3.9/
| |
| − | src/rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | src/rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git add src/dock/orient.cpp
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git commit -m "feat: shows number of spheres generated"
| |
| − | [alpha_branch 704ff10f] feat: shows number of spheres generated
| |
| − | 1 file changed, 3 insertions(+), 3 deletions(-)
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git add src/rdkit/Makefile
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git commit -m "fix: replaces boost url with working one "
| |
| − | [alpha_branch 123e4913] fix: replaces boost url with working one
| |
| − | 1 file changed, 3 insertions(+), 1 deletion(-)
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch and 'origin/alpha_branch' have diverged,
| |
| − | and have 3 and 267 different commits each, respectively.
| |
| − | (use "git pull" if you want to integrate the remote branch with yours)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add/rm <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | deleted: install/test/minimization/minimize7.dockout
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | src/dock/lol
| |
| − | src/rdkit/boost/
| |
| − | src/rdkit/boost_1_71_0.tar.gz
| |
| − | src/rdkit/boost_1_71_0/
| |
| − | src/rdkit/eigen-3.3.9.tar.gz
| |
| − | src/rdkit/eigen-3.3.9/
| |
| − | src/rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | src/rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git push
| |
| − | Username for 'https://github.com': EvanS-Dock6
| |
| − | Password for 'https://EvanS-Dock6@github.com':
| |
| − | remote: Support for password authentication was removed on August 13, 2021.
| |
| − | remote: Please see https://docs.github.com/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication.
| |
| − | fatal: Authentication failed for 'https://github.com/EvanS-Dock6/dock6.git/'
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git push
| |
| − | Username for 'https://github.com': EvanS-Dock6
| |
| − | Password for 'https://EvanS-Dock6@github.com':
| |
| − | To https://github.com/EvanS-Dock6/dock6.git
| |
| − | ! [rejected] alpha_branch -> alpha_branch (non-fast-forward)
| |
| − | error: failed to push some refs to 'https://github.com/EvanS-Dock6/dock6.git'
| |
| − | hint: Updates were rejected because the tip of your current branch is behind
| |
| − | hint: its remote counterpart. If you want to integrate the remote changes,
| |
| − | hint: use 'git pull' before pushing again.
| |
| − | hint: See the 'Note about fast-forwards' in 'git push --help' for details.
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git pull
| |
| − | Username for 'https://github.com': EvanS-Dock6
| |
| − | Password for 'https://EvanS-Dock6@github.com':
| |
| − | hint: You have divergent branches and need to specify how to reconcile them.
| |
| − | hint: You can do so by running one of the following commands sometime before
| |
| − | hint: your next pull:
| |
| − | hint:
| |
| − | hint: git config pull.rebase false # merge
| |
| − | hint: git config pull.rebase true # rebase
| |
| − | hint: git config pull.ff only # fast-forward only
| |
| − | hint:
| |
| − | hint: You can replace "git config" with "git config --global" to set a default
| |
| − | hint: preference for all repositories. You can also pass --rebase, --no-rebase,
| |
| − | hint: or --ff-only on the command line to override the configured default per
| |
| − | hint: invocation.
| |
| − | fatal: Need to specify how to reconcile divergent branches.
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git pull --rebase
| |
| − | error: cannot pull with rebase: You have unstaged changes.
| |
| − | error: Please commit or stash them.
| |
| − | (base) [ehspector@milan2 alpha_branch]$ ls
| |
| − | bin docs parameters README.md template_pipeline
| |
| − | developer install README src tutorials
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch and 'origin/alpha_branch' have diverged,
| |
| − | and have 3 and 267 different commits each, respectively.
| |
| − | (use "git pull" if you want to integrate the remote branch with yours)
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add/rm <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | deleted: install/test/minimization/minimize7.dockout
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | src/dock/lol
| |
| − | src/rdkit/boost/
| |
| − | src/rdkit/boost_1_71_0.tar.gz
| |
| − | src/rdkit/boost_1_71_0/
| |
| − | src/rdkit/eigen-3.3.9.tar.gz
| |
| − | src/rdkit/eigen-3.3.9/
| |
| − | src/rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | src/rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git rm install/test/minimization/minimize7.dockout
| |
| − | rm 'install/test/minimization/minimize7.dockout'
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch and 'origin/alpha_branch' have diverged,
| |
| − | and have 3 and 267 different commits each, respectively.
| |
| − | (use "git pull" if you want to integrate the remote branch with yours)
| |
| − |
| |
| − | Changes to be committed:
| |
| − | (use "git restore --staged <file>..." to unstage)
| |
| − | deleted: install/test/minimization/minimize7.dockout
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | src/dock/lol
| |
| − | src/rdkit/boost/
| |
| − | src/rdkit/boost_1_71_0.tar.gz
| |
| − | src/rdkit/boost_1_71_0/
| |
| − | src/rdkit/eigen-3.3.9.tar.gz
| |
| − | src/rdkit/eigen-3.3.9/
| |
| − | src/rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | src/rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git commit -m "build: rm minimize.docot"
| |
| − | [alpha_branch fe018e1e] build: rm minimize.docot
| |
| − | 1 file changed, 187 deletions(-)
| |
| − | delete mode 100644 install/test/minimization/minimize7.dockout
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git push
| |
| − | Username for 'https://github.com': ^C
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git pull
| |
| − | Username for 'https://github.com': EvanS-Dock6
| |
| − | Password for 'https://EvanS-Dock6@github.com':
| |
| − | hint: You have divergent branches and need to specify how to reconcile them.
| |
| − | hint: You can do so by running one of the following commands sometime before
| |
| − | hint: your next pull:
| |
| − | hint:
| |
| − | hint: git config pull.rebase false # merge
| |
| − | hint: git config pull.rebase true # rebase
| |
| − | hint: git config pull.ff only # fast-forward only
| |
| − | hint:
| |
| − | hint: You can replace "git config" with "git config --global" to set a default
| |
| − | hint: preference for all repositories. You can also pass --rebase, --no-rebase,
| |
| − | hint: or --ff-only on the command line to override the configured default per
| |
| − | hint: invocation.
| |
| − | fatal: Need to specify how to reconcile divergent branches.
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git pull --rebase
| |
| − | Username for 'https://github.com': EvanS-Dock6
| |
| − | Password for 'https://EvanS-Dock6@github.com':
| |
| − | Successfully rebased and updated refs/heads/alpha_branch.
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch is ahead of 'origin/alpha_branch' by 4 commits.
| |
| − | (use "git push" to publish your local commits)
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | src/dock/lol
| |
| − | src/rdkit/boost/
| |
| − | src/rdkit/boost_1_71_0.tar.gz
| |
| − | src/rdkit/boost_1_71_0/
| |
| − | src/rdkit/eigen-3.3.9.tar.gz
| |
| − | src/rdkit/eigen-3.3.9/
| |
| − | src/rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | src/rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | nothing added to commit but untracked files present (use "git add" to track)
| |
| − | (base) [ehspector@milan2 alpha_branch]$ git push
| |
| − | Username for 'https://github.com': EvanS-Dock6
| |
| − | Password for 'https://EvanS-Dock6@github.com':
| |
| − | Enumerating objects: 34, done.
| |
| − | Counting objects: 100% (34/34), done.
| |
| − | Delta compression using up to 128 threads
| |
| − | Compressing objects: 100% (21/21), done.
| |
| − | Writing objects: 100% (22/22), 2.96 KiB | 2.96 MiB/s, done.
| |
| − | Total 22 (delta 17), reused 0 (delta 0), pack-reused 0
| |
| − | remote: Resolving deltas: 100% (17/17), completed with 11 local objects.
| |
| − | To https://github.com/EvanS-Dock6/dock6.git
| |
| − | 2ce698b4..5f99310b alpha_branch -> alpha_branch
| |
| − | (base) [ehspector@milan2 alpha_branch]$ docs
| |
| − | -bash: docs: command not found
| |
| − | (base) [ehspector@milan2 alpha_branch]$ cd docs
| |
| − | (base) [ehspector@milan2 docs]$ ls
| |
| − | bugfixes610 bugfixes65 dock6_manual.html new_in_6.11.txt new_in_6.4.txt README
| |
| − | bugfixes611 bugfixes66 faq new_in_6.12.txt new_in_6.5.txt tutorials
| |
| − | bugfixes612 bugfixes67 faq.htm new_in_6.13.txt new_in_6.6.txt
| |
| − | bugfixes62 bugfixes68 images new_in_6.1.txt new_in_6.7.txt
| |
| − | bugfixes63 bugfixes69 index.htm new_in_6.2.txt new_in_6.8.txt
| |
| − | bugfixes64 bugfixes.htm new_in_6.10.txt new_in_6.3.txt new_in_6.9.txt
| |
| − | (base) [ehspector@milan2 docs]$ vi new_in_6.13.txt
| |
| − | (base) [ehspector@milan2 docs]$ home
| |
| − | (base) [ehspector@milan2 espector]$ cd 4s0v/gas_teiger/
| |
| − | (base) [ehspector@milan2 gas_teiger]$ vi gas.in
| |
| − | (base) [ehspector@milan2 gas_teiger]$ home
| |
| − | (base) [ehspector@milan2 espector]$ cd builds/alpha_branch/docs
| |
| − | (base) [ehspector@milan2 docs]$ vi new_in_6.13.txt
| |
| − | (base) [ehspector@milan2 docs]$ vi dock6_manual.html
| |
| − | (base) [ehspector@milan2 docs]$ pwd
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/docs
| |
| − | (base) [ehspector@milan2 docs]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ home
| |
| − | (base) [ehspector@milan2 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@milan2 espector]$ cd ..
| |
| − | (base) [ehspector@milan2 rizzo]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project class_work
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd class_work/
| |
| − | (base) [ehspector@milan2 class_work]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 class_work]$ cd 001_structure/
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | 2w26_ligand_hydrogens_charges.mol2 2w26_protein_no_hydrogens_no_charges.mol2
| |
| − | 2w26_ligand_no_hydrogens_no_charges.mol2 2w26_protein_with_charges.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26_new_surface.dms 2w26.sph INSPH OUTSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi 2w26.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26_new_surface.dms 2w26.sph INSPH OUTSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/sphere_selector 2w26.sph ../001_structure/2w26_ligand_hydrogens_charges.mol2 10.0
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26_new_surface.dms 2w26.sph INSPH OUTSPH selected_spheres.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26_new_surface.dms 2w26.sph INSPH OUTSPH selected_spheres.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ rm 2w26.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26_new_surface.dms 2w26.sph INSPH OUTSPH selected_spheres.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ cd 003
| |
| − | -bash: cd: 003: No such file or directory
| |
| − | (base) [ehspector@milan2 class_work]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ cd 002
| |
| − | -bash: cd: 002: No such file or directory
| |
| − | (base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi showbox.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 01showbox.sh showbox.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
| |
| − | automatically construct box to enclose spheres [Y/N]?
| |
| − | extra margin to also be enclosed (angstroms)?
| |
| − | (this will be added in all 6 directions)
| |
| − | sphere file-
| |
| − | cluster number-
| |
| − | At line 61 of file showbox.f (unit = 1)
| |
| − | Fortran runtime error: Cannot open file '../002_spheres/selected_spheres.sph': No such file or directory
| |
| − |
| |
| − | Error termination. Backtrace:
| |
| − | #0 0x7ffff7d54ca5 in already_open
| |
| − | at ../../../libgfortran/io/open.c:742
| |
| − | #1 0x4015d9 in ???
| |
| − | #2 0x40115c in ???
| |
| − | #3 0x7ffff742958f in ???
| |
| − | #4 0x7ffff742963f in ???
| |
| − | #5 0x401194 in ???
| |
| − | #6 0xffffffffffffffff in ???
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 01showbox.sh showbox.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26_new_surface.dms 2w26.sph INSPH OUTSPH selected_spheres.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ cd 003
| |
| − | -bash: cd: 003: No such file or directory
| |
| − | (base) [ehspector@milan2 class_work]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 01showbox.sh showbox.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi showbox.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi showbox.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
| |
| − | 01showbox.sh: line 3: syntax error near unexpected token `&'
| |
| − | 01showbox.sh: line 3: `/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/showbox < &showbox.in&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
| |
| − | 01showbox.sh: line 3: syntax error near unexpected token `&'
| |
| − | 01showbox.sh: line 3: `/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/showbox < showbox.in > &showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi 01showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ bash 01showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 01showbox.sh 2w26.box.pdb showbox.in '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi showbox.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 01showbox.sh 2w26.box.pdb showbox.in '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi 2w26.box.pdb
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ cd ..
| |
| − | (base) [ehspector@milan2 AMS_536]$ tar -cvf 2w26
| |
| − | tar: Cowardly refusing to create an empty archive
| |
| − | Try 'tar --help' or 'tar --usage' for more information.
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project class_work
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd class_
| |
| − | -bash: cd: class_: No such file or directory
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd class_work/
| |
| − | (base) [ehspector@milan2 class_work]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 class_work]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 class_work]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 01showbox.sh 2w26.box.pdb showbox.in '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ cd 001_structure/
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | 2w26_ligand_hydrogens_charges.mol2 2w26_protein_no_hydrogens_no_charges.mol2
| |
| − | 2w26_ligand_no_hydrogens_no_charges.mol2 2w26_protein_with_charges.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 01showbox.sh 2w26.box.pdb grid.in grid.sh showbox.in '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ bash grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 01showbox.sh 2w26.box.pdb grid.in grid.out grid.sh showbox.in '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.out
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 class_work]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 01showbox.sh 2w26.box.pdb grid.in grid.out grid.sh showbox.in '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ bash grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 01showbox.sh 2w26.box.pdb grid.in grid.out grid.sh showbox.in '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.out
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 class_work]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 class_work]$ cd 001_structure/
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | 2w26_ligand_hydrogens_charges.mol2 2w26_protein_no_hydrogens_no_charges.mol2
| |
| − | 2w26_ligand_no_hydrogens_no_charges.mol2 2w26_protein_with_charges.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ vi 2w26_protein_with_charges.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ pwd
| |
| − | /gpfs/home/ehspector/AMS_536/class_work/001_structure
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| − | (base) [ehspector@milan2 001_structure]$ homw
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| − | -bash: homw: command not found
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| − | (base) [ehspector@milan2 001_structure]$ home
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| − | (base) [ehspector@milan2 espector]$ ls
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| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
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| − | (base) [ehspector@milan2 espector]$ cd gas_test/
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| − | (base) [ehspector@milan2 gas_test]$ ls
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| − | 4s0v_GA.in 4s0v_GA_output.restart0028.mol2
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| − | 4s0v_GA.out 4s0v_GA_output.restart0029.mol2
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| − | 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2
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| − | 4s0v_GA_output.restart0001.mol2 4s0v_GA_output.restart0031.mol2
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| − | 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2
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| − | 4s0v_GA_output.restart0003.mol2 4s0v_GA_output.restart0033.mol2
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| − | 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2
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| − | 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2
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| − | 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2
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| − | 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2
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| − | 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2
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| − | 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2
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| − | 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2
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| − | 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2
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| − | 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2
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| − | 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2
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| − | 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2
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| − | 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2
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| − | 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2
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| − | 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2
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| − | 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2
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| − | 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2
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| − | 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2
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| − | 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm
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| − | 4s0v_GA_output.restart0022.mol2 charge_data
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| − | 4s0v_GA_output.restart0023.mol2 gas_f_test
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| − | 4s0v_GA_output.restart0024.mol2 gas_RD_Test
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| − | 4s0v_GA_output.restart0025.mol2 GA.txt
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| − | 4s0v_GA_output.restart0026.mol2 test_2.in
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| − | 4s0v_GA_output.restart0027.mol2 test.in
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| − | (base) [ehspector@milan2 gas_test]$ cd ..
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| − | (base) [ehspector@milan2 espector]$ ls
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| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
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| − | (base) [ehspector@milan2 espector]$ cd gas_test/
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| − | (base) [ehspector@milan2 gas_test]$ vi test.in
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| − | (base) [ehspector@milan2 gas_test]$ vi test_2.in
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| − | (base) [ehspector@milan2 gas_test]$ cd gas_f_test/
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| − | (base) [ehspector@milan2 gas_f_test]$ ls
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| − | diff.out gas_0.out_scored.mol2 gas_1.out gas_50.in gas_50.out_scored.mol2
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| − | gas_0.out gas_1.in gas_1.out_scored.mol2 gas_50.out
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| − | (base) [ehspector@milan2 gas_f_test]$ vi gas_1.in
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| − | (base) [ehspector@milan2 gas_f_test]$ cd ..
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| − | (base) [ehspector@milan2 gas_test]$ cd ..
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| − | (base) [ehspector@milan2 espector]$ ls
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| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
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| − | (base) [ehspector@milan2 espector]$ cd gas_test/
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| − | (base) [ehspector@milan2 gas_test]$ ls
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| − | 4s0v_GA.in 4s0v_GA_output.restart0028.mol2
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| − | 4s0v_GA.out 4s0v_GA_output.restart0029.mol2
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| − | 4s0v_GA_output.restart0000.mol2 4s0v_GA_output.restart0030.mol2
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| − | 4s0v_GA_output.restart0002.mol2 4s0v_GA_output.restart0032.mol2
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| − | 4s0v_GA_output.restart0004.mol2 4s0v_GA_output.restart0034.mol2
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| − | 4s0v_GA_output.restart0005.mol2 4s0v_GA_output.restart0035.mol2
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| − | 4s0v_GA_output.restart0006.mol2 4s0v_GA_output.restart0036.mol2
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| − | 4s0v_GA_output.restart0007.mol2 4s0v_GA_output.restart0037.mol2
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| − | 4s0v_GA_output.restart0008.mol2 4s0v_GA_output.restart0038.mol2
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| − | 4s0v_GA_output.restart0009.mol2 4s0v_GA_output.restart0039.mol2
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| − | 4s0v_GA_output.restart0010.mol2 4s0v_GA_output.restart0040.mol2
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| − | 4s0v_GA_output.restart0011.mol2 4s0v_GA_output.restart0041.mol2
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| − | 4s0v_GA_output.restart0012.mol2 4s0v_GA_output.restart0042.mol2
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| − | 4s0v_GA_output.restart0013.mol2 4s0v_GA_output.restart0043.mol2
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| − | 4s0v_GA_output.restart0014.mol2 4s0v_GA_output.restart0044.mol2
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| − | 4s0v_GA_output.restart0015.mol2 4s0v_GA_output.restart0045.mol2
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| − | 4s0v_GA_output.restart0016.mol2 4s0v_GA_output.restart0046.mol2
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| − | 4s0v_GA_output.restart0017.mol2 4s0v_GA_output.restart0047.mol2
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| − | 4s0v_GA_output.restart0018.mol2 4s0v_GA_output.restart0048.mol2
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| − | 4s0v_GA_output.restart0019.mol2 4s0v_GA_output.restart0049.mol2
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| − | 4s0v_GA_output.restart0020.mol2 4s0v_GA_output.restart0050.mol2
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| − | 4s0v_GA_output.restart0021.mol2 4s0v_GA.slurm
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| − | 4s0v_GA_output.restart0022.mol2 charge_data
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| − | 4s0v_GA_output.restart0023.mol2 gas_f_test
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| − | 4s0v_GA_output.restart0024.mol2 gas_RD_Test
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| − | 4s0v_GA_output.restart0025.mol2 GA.txt
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| − | 4s0v_GA_output.restart0026.mol2 test_2.in
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| − | 4s0v_GA_output.restart0027.mol2 test.in
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| − | (base) [ehspector@milan2 gas_test]$ cd gas_f_test/
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| − | (base) [ehspector@milan2 gas_f_test]$ ls
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| − | diff.out gas_0.out_scored.mol2 gas_1.out gas_50.in gas_50.out_scored.mol2
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| − | gas_0.out gas_1.in gas_1.out_scored.mol2 gas_50.out
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| − | (base) [ehspector@milan2 gas_f_test]$ cp gas_1.in gas_2.in
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| − | (base) [ehspector@milan2 gas_f_test]$ vi gas_2.in
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| − | (base) [ehspector@milan2 gas_f_test]$ vi gas_2.in
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| − | (base) [ehspector@milan2 gas_f_test]$ dock6 -i gas_2.in -o gas_2.out
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| − | ^C
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| − | (base) [ehspector@milan2 gas_f_test]$ ls
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| − | diff.out gas_1.in gas_2.in gas_50.out
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| − | gas_0.out gas_1.out gas_2.out gas_50.out_scored.mol2
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| − | gas_0.out_scored.mol2 gas_1.out_scored.mol2 gas_50.in gas.out_scored.mol2
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| − | (base) [ehspector@milan2 gas_f_test]$ vi gas_2.out
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| − | (base) [ehspector@milan2 gas_f_test]$ home
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| − | (base) [ehspector@milan2 espector]$ ls
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| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
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| − | (base) [ehspector@milan2 espector]$ cd builds/alpha_branch/docs/
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| − | (base) [ehspector@milan2 docs]$ ls
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| − | bugfixes610 bugfixes65 dock6_manual.html new_in_6.11.txt new_in_6.4.txt README
| |
| − | bugfixes611 bugfixes66 faq new_in_6.12.txt new_in_6.5.txt tutorials
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| − | bugfixes612 bugfixes67 faq.htm new_in_6.13.txt new_in_6.6.txt
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| − | bugfixes62 bugfixes68 images new_in_6.1.txt new_in_6.7.txt
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| − | bugfixes63 bugfixes69 index.htm new_in_6.2.txt new_in_6.8.txt
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| − | bugfixes64 bugfixes.htm new_in_6.10.txt new_in_6.3.txt new_in_6.9.txt
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| − | (base) [ehspector@milan2 docs]$ vi new_in_6.13.txt
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| − | (base) [ehspector@milan2 docs]$ class
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| − | (base) [ehspector@milan2 AMS_536]$ mkdir 1086 5EEN
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| − | (base) [ehspector@milan2 AMS_536]$ ls
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| − | 1086 5EEN class_project class_work
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| − | (base) [ehspector@milan2 AMS_536]$ exit
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| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
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| − | (base) supremestudier@Evans-MBP Spring_25 % cd AMS_536/Tutorial
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ls
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| − | 2w26.box.pdb
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| − | 2w26.pdb
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| − | 2w26.pdb1.gz
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| − | 2w26.sph
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| − | 2w26_charges.pdb
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| − | 2w26_ligand.pdb
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| − | 2w26_ligand_hydrogens_charges.mol2
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| − | 2w26_ligand_hydrogens_charges.pdb
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| − | 2w26_ligand_no_hydrogens_no_charges.mol2
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| − | 2w26_new_surface.dms
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| − | 2w26_protein_no_hydrogens_no_charges.mol2
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| − | 2w26_protein_only.pdb
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| − | 2w26_protein_with_charges.mol2
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| − | 2w26_surface.dms
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| − | selected_spheres.sph
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| − | (base) supremestudier@Evans-MBP Tutorial % vi 2w26.pdb
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| − | (base) supremestudier@Evans-MBP Tutorial % ls
| |
| − | 2w26.box.pdb
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| − | 2w26.pdb
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| − | 2w26.pdb1.gz
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| − | 2w26.sph
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| − | 2w26_charges.pdb
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| − | 2w26_ligand.pdb
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| − | 2w26_ligand_hydrogens_charges.mol2
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| − | 2w26_ligand_hydrogens_charges.pdb
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| − | 2w26_ligand_no_hydrogens_no_charges.mol2
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| − | 2w26_new_surface.dms
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| − | 2w26_protein_no_hydrogens_no_charges.mol2
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| − | 2w26_protein_only.pdb
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| − | 2w26_protein_with_charges.mol2
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| − | 2w26_surface.dms
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| − | selected_spheres.sph
| |
| − | (base) supremestudier@Evans-MBP Tutorial % mdkir 2w26
| |
| − | zsh: command not found: mdkir
| |
| − | (base) supremestudier@Evans-MBP Tutorial % mkdir 2w26
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ls
| |
| − | 2w26
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| − | 2w26.box.pdb
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| − | 2w26.pdb
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| − | 2w26.pdb1.gz
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| − | 2w26.sph
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| − | 2w26_charges.pdb
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| − | 2w26_ligand.pdb
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| − | 2w26_ligand_hydrogens_charges.mol2
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| − | 2w26_ligand_hydrogens_charges.pdb
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| − | 2w26_ligand_no_hydrogens_no_charges.mol2
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| − | 2w26_new_surface.dms
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| − | 2w26_protein_no_hydrogens_no_charges.mol2
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| − | 2w26_protein_only.pdb
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| − | 2w26_protein_with_charges.mol2
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| − | 2w26_surface.dms
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| − | selected_spheres.sph
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| − | (base) supremestudier@Evans-MBP Tutorial % cd ..
| |
| − | (base) supremestudier@Evans-MBP AMS_536 % cd ..
| |
| − | (base) supremestudier@Evans-MBP Spring_25 % cd AMS_548
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ls
| |
| − | Polaris.ipynb ligand_poses_reference_structures.zip
| |
| − | ligand_poses_reference_structures
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % pwd
| |
| − | /Users/supremestudier/Desktop/GradSchool/StonyBrook/Semester/Spring_25/AMS_548
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % pip install pymol
| |
| − | ERROR: Could not find a version that satisfies the requirement pymol (from versions: none)
| |
| − | ERROR: No matching distribution found for pymol
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % which python
| |
| − | /Users/supremestudier/anaconda3/bin/python
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % tar -jxf pymol-X_XX-bin-linux-x86-glibc23.tar.bz2
| |
| − | tar: Error opening archive: Failed to open 'pymol-X_XX-bin-linux-x86-glibc23.tar.bz2'
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % conda install -c conda-forge -c schrodinger pymol-bundle
| |
| − | Retrieving notices: ...working... done
| |
| − | Collecting package metadata (current_repodata.json): - WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
| |
| − | done
| |
| − | Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
| |
| − | Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
| |
| − | Collecting package metadata (repodata.json): / WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
| |
| − | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
| |
| − | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0
| |
| − | done
| |
| − | Solving environment: - unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
| |
| − |
| |
| − | CondaError: KeyboardInterrupt
| |
| − |
| |
| − |
| |
| − | (base) supremestudier@Evans-MBP AMS_548 %
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U
| |
| − | Collecting boltz
| |
| − | Obtaining dependency information for boltz from https://files.pythonhosted.org/packages/22/b3/6bbc7aaea024d3dc13abc8e94ee32df74dd63bfc016e0f87abd20d0dcbbd/boltz-0.4.1-py3-none-any.whl.metadata
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| − | Downloading boltz-0.4.1-py3-none-any.whl.metadata (4.8 kB)
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| − | Collecting torch>=2.2 (from boltz)
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| − | Obtaining dependency information for torch>=2.2 from https://files.pythonhosted.org/packages/3f/14/e105b8ef6d324e789c1589e95cb0ab63f3e07c2216d68b1178b7c21b7d2a/torch-2.2.2-cp311-none-macosx_10_9_x86_64.whl.metadata
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| − | Downloading torch-2.2.2-cp311-none-macosx_10_9_x86_64.whl.metadata (25 kB)
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| − | Collecting numpy==1.26.3 (from boltz)
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| − | Obtaining dependency information for numpy==1.26.3 from https://files.pythonhosted.org/packages/42/db/82cc805d96ba48622fbb7395a7b44cf59567fca235e397cdf64555081773/numpy-1.26.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata
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| − | Downloading numpy-1.26.3-cp311-cp311-macosx_10_9_x86_64.whl.metadata (61 kB)
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| − | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 1.2 MB/s eta 0:00:00
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| − | Collecting hydra-core==1.3.2 (from boltz)
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| − | Obtaining dependency information for hydra-core==1.3.2 from https://files.pythonhosted.org/packages/c6/50/e0edd38dcd63fb26a8547f13d28f7a008bc4a3fd4eb4ff030673f22ad41a/hydra_core-1.3.2-py3-none-any.whl.metadata
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| − | Downloading hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)
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| − | Collecting pytorch-lightning==2.4.0 (from boltz)
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| − | Obtaining dependency information for pytorch-lightning==2.4.0 from https://files.pythonhosted.org/packages/2b/d2/ecd65ff1e0b1ca79f9785dd65d5ced7ec2643a828068aaa24e47e4c84a14/pytorch_lightning-2.4.0-py3-none-any.whl.metadata
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| − | Downloading pytorch_lightning-2.4.0-py3-none-any.whl.metadata (21 kB)
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| − | Requirement already satisfied: rdkit>=2024.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2024.9.4)
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| − | Collecting dm-tree==0.1.8 (from boltz)
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| − | Obtaining dependency information for dm-tree==0.1.8 from https://files.pythonhosted.org/packages/b1/65/4f10a68dde5fa0c91043c9c899e9bc79b1657ba932d39a5f8525c0058e68/dm_tree-0.1.8-cp311-cp311-macosx_10_9_x86_64.whl.metadata
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| − | Downloading dm_tree-0.1.8-cp311-cp311-macosx_10_9_x86_64.whl.metadata (1.9 kB)
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| − | Collecting requests==2.32.3 (from boltz)
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| − | Obtaining dependency information for requests==2.32.3 from https://files.pythonhosted.org/packages/f9/9b/335f9764261e915ed497fcdeb11df5dfd6f7bf257d4a6a2a686d80da4d54/requests-2.32.3-py3-none-any.whl.metadata
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| − | Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
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| − | Requirement already satisfied: pandas>=2.2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.3)
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| − | Collecting types-requests (from boltz)
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| − | Obtaining dependency information for types-requests from https://files.pythonhosted.org/packages/d7/01/485b3026ff90e5190b5e24f1711522e06c79f4a56c8f4b95848ac072e20f/types_requests-2.32.0.20241016-py3-none-any.whl.metadata
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| − | Downloading types_requests-2.32.0.20241016-py3-none-any.whl.metadata (1.9 kB)
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| − | Collecting einops==0.8.0 (from boltz)
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| − | Obtaining dependency information for einops==0.8.0 from https://files.pythonhosted.org/packages/44/5a/f0b9ad6c0a9017e62d4735daaeb11ba3b6c009d69a26141b258cd37b5588/einops-0.8.0-py3-none-any.whl.metadata
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| − | Downloading einops-0.8.0-py3-none-any.whl.metadata (12 kB)
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| − | Collecting einx==0.3.0 (from boltz)
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| − | Obtaining dependency information for einx==0.3.0 from https://files.pythonhosted.org/packages/90/04/4a730d74fd908daad86d6b313f235cdf8e0cf1c255b392b7174ff63ea81a/einx-0.3.0-py3-none-any.whl.metadata
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| − | Downloading einx-0.3.0-py3-none-any.whl.metadata (6.9 kB)
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| − | Collecting fairscale==0.4.13 (from boltz)
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| − | Downloading fairscale-0.4.13.tar.gz (266 kB)
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| − | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 64.9/64.9 kB 2.1 MB/s eta 0:00:00
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| − | Downloading torch-2.2.2-cp311-none-macosx_10_9_x86_64.whl (150.8 MB)
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| − | Downloading types_requests-2.32.0.20241016-py3-none-any.whl (15 kB)
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| − | Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
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| − | Downloading GitPython-3.1.44-py3-none-any.whl (207 kB)
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| − | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 207.6/207.6 kB 5.2 MB/s eta 0:00:00
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| − | Downloading lightning_utilities-0.12.0-py3-none-any.whl (28 kB)
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| − | Downloading omegaconf-2.3.0-py3-none-any.whl (79 kB)
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| − | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 79.5/79.5 kB 2.4 MB/s eta 0:00:00
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| − | Downloading sentry_sdk-2.20.0-py2.py3-none-any.whl (322 kB)
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| − | Downloading torchmetrics-1.6.1-py3-none-any.whl (927 kB)
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| − | Downloading urllib3-2.3.0-py3-none-any.whl (128 kB)
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| − | Downloading frozendict-2.4.6-py311-none-any.whl (16 kB)
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| − | Downloading smmap-5.0.2-py3-none-any.whl (24 kB)
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| − | Building wheels for collected packages: fairscale, modelcif, antlr4-python3-runtime, ihm
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| − | Building wheel for fairscale (pyproject.toml) ... done
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| − | Created wheel for fairscale: filename=fairscale-0.4.13-py3-none-any.whl size=332156 sha256=3ede1c2291f5f6b09d62a36695c4c9250859b36c640d9fcd0e2ddf99fb7a7ce3
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| − | Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/95/ef/96/5044bde220b2ea299bdc6ec05051e0ef187fad45b341d1c273
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| − | Building wheel for modelcif (setup.py) ... done
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| − | Created wheel for modelcif: filename=modelcif-1.2-py3-none-any.whl size=41187 sha256=ffeb8ba2c058dca784bb74a9e91f3210826944eeaece3de4c80c69a9f5659770
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| − | Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/d2/3a/8c/e28cb28a15568d1b1b6163c77c945a5961351340fd15b9b4df
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| − | Building wheel for antlr4-python3-runtime (setup.py) ... done
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| − | Created wheel for antlr4-python3-runtime: filename=antlr4_python3_runtime-4.9.3-py3-none-any.whl size=144554 sha256=5a4205dda4ab01f28989906b79caaca2658ccbd40e312bfcea5dd139ba8f310e
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| − | Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/1a/97/32/461f837398029ad76911109f07047fde1d7b661a147c7c56d1
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| − | Building wheel for ihm (setup.py) ... done
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| − | Created wheel for ihm: filename=ihm-1.8-cp311-cp311-macosx_10_9_x86_64.whl size=194880 sha256=4937e5d722d0d8f12b399d018666e98e070d6821743b4275bb68fed2605a2a06
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| − | Stored in directory: /Users/supremestudier/Library/Caches/pip/wheels/04/b2/4d/f14324777ef987a2137e6bd184eab20679aeadf9d3ad67d198
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| − | Successfully built fairscale modelcif antlr4-python3-runtime ihm
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| − | Installing collected packages: dm-tree, antlr4-python3-runtime, urllib3, smmap, setproctitle, pyyaml, numpy, mashumaro, lightning-utilities, ihm, frozendict, einops, docker-pycreds, click, types-requests, torch, sentry-sdk, scipy, requests, omegaconf, modelcif, gitdb, einx, biopython, torchmetrics, hydra-core, gitpython, fairscale, wandb, pytorch-lightning, boltz
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| − | Attempting uninstall: urllib3
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| − | Found existing installation: urllib3 1.26.16
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| − | Uninstalling urllib3-1.26.16:
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| − | Successfully uninstalled urllib3-1.26.16
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| − | Attempting uninstall: pyyaml
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| − | Found existing installation: PyYAML 6.0
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| − | Uninstalling PyYAML-6.0:
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| − | Successfully uninstalled PyYAML-6.0
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| − | Attempting uninstall: numpy
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| − | Found existing installation: numpy 1.26.4
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| − | Uninstalling numpy-1.26.4:
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| − | Successfully uninstalled numpy-1.26.4
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| − | Attempting uninstall: click
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| − | Found existing installation: click 8.0.4
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| − | Uninstalling click-8.0.4:
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| − | Successfully uninstalled click-8.0.4
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| − | Attempting uninstall: scipy
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| − | Found existing installation: scipy 1.15.1
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| − | Uninstalling scipy-1.15.1:
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| − | Successfully uninstalled scipy-1.15.1
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| − | Attempting uninstall: requests
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| − | Found existing installation: requests 2.31.0
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| − | Uninstalling requests-2.31.0:
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| − | Successfully uninstalled requests-2.31.0
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| − | ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
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| − | tables 3.8.0 requires blosc2~=2.0.0, which is not installed.
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| − | tables 3.8.0 requires cython>=0.29.21, which is not installed.
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| − | conda-repo-cli 1.0.75 requires requests_mock, which is not installed.
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| − | spyder 5.4.3 requires pyqt5<5.16, which is not installed.
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| − | spyder 5.4.3 requires pyqtwebengine<5.16, which is not installed.
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| − | gensim 4.3.0 requires FuzzyTM>=0.4.0, which is not installed.
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| − | conda-repo-cli 1.0.75 requires clyent==1.2.1, but you have clyent 1.2.2 which is incompatible.
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| − | conda-repo-cli 1.0.75 requires PyYAML==6.0.1, but you have pyyaml 6.0.2 which is incompatible.
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| − | conda-repo-cli 1.0.75 requires requests==2.31.0, but you have requests 2.32.3 which is incompatible.
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| − | numba 0.57.0 requires numpy<1.25,>=1.21, but you have numpy 1.26.3 which is incompatible.
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| − | python-lsp-black 1.2.1 requires black>=22.3.0, but you have black 0.0 which is incompatible.
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| − | anaconda-cloud-auth 0.1.3 requires pydantic<2.0, but you have pydantic 2.10.6 which is incompatible.
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| − | aiobotocore 2.5.0 requires botocore<1.29.77,>=1.29.76, but you have botocore 1.35.99 which is incompatible.
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| − | Successfully installed antlr4-python3-runtime-4.9.3 biopython-1.84 boltz-0.4.1 click-8.1.7 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0 einx-0.3.0 fairscale-0.4.13 frozendict-2.4.6 gitdb-4.0.12 gitpython-3.1.44 hydra-core-1.3.2 ihm-1.8 lightning-utilities-0.12.0 mashumaro-3.14 modelcif-1.2 numpy-1.26.3 omegaconf-2.3.0 pytorch-lightning-2.4.0 pyyaml-6.0.2 requests-2.32.3 scipy-1.13.1 sentry-sdk-2.20.0 setproctitle-1.3.4 smmap-5.0.2 torch-2.2.2 torchmetrics-1.6.1 types-requests-2.32.0.20241016 urllib3-2.3.0 wandb-0.18.7
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| − | (base) supremestudier@Evans-MBP AMS_548 % pip install --upgrade pip
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| − |
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| − | Requirement already satisfied: pip in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (23.2.1)
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| − | Collecting pip
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| − | Obtaining dependency information for pip from https://files.pythonhosted.org/packages/85/8a/1ddf40be20103bcc605db840e9ade09c8e8c9f920a03e9cfe88eae97a058/pip-25.0-py3-none-any.whl.metadata
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| − | Downloading pip-25.0-py3-none-any.whl.metadata (3.7 kB)
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| − | Downloading pip-25.0-py3-none-any.whl (1.8 MB)
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| − | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 10.9 MB/s eta 0:00:00
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| − | Installing collected packages: pip
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| − | Attempting uninstall: pip
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| − | Found existing installation: pip 23.2.1
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| − | Uninstalling pip-23.2.1:
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| − | Successfully uninstalled pip-23.2.1
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| − | Successfully installed pip-25.0
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| − | (base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U
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| − | Requirement already satisfied: boltz in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (0.4.1)
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| − | Requirement already satisfied: torch>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.2)
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| − | Requirement already satisfied: numpy==1.26.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.26.3)
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| − | Requirement already satisfied: hydra-core==1.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.3.2)
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| − | Requirement already satisfied: pytorch-lightning==2.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.4.0)
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| − | Requirement already satisfied: rdkit>=2024.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2024.9.4)
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| − | Requirement already satisfied: dm-tree==0.1.8 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.1.8)
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| − | Requirement already satisfied: requests==2.32.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.3)
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| − | Requirement already satisfied: pandas>=2.2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.3)
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| − | Requirement already satisfied: types-requests in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.0.20241016)
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| − | Requirement already satisfied: einops==0.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.8.0)
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| − | Requirement already satisfied: einx==0.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.3.0)
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| − | Requirement already satisfied: fairscale==0.4.13 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.4.13)
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| − | Requirement already satisfied: mashumaro==3.14 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (3.14)
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| − | Requirement already satisfied: modelcif==1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.2)
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| − | Requirement already satisfied: wandb==0.18.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.18.7)
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| − | Requirement already satisfied: click==8.1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (8.1.7)
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| − | Requirement already satisfied: pyyaml==6.0.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (6.0.2)
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| − | Requirement already satisfied: biopython==1.84 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.84)
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| − | Requirement already satisfied: scipy==1.13.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.13.1)
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| − | Requirement already satisfied: sympy in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (1.11.1)
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| − | Requirement already satisfied: frozendict in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (2.4.6)
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| − | Requirement already satisfied: omegaconf<2.4,>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (2.3.0)
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| − | Requirement already satisfied: antlr4-python3-runtime==4.9.* in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (4.9.3)
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| − | Requirement already satisfied: packaging in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (23.1)
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| − | Requirement already satisfied: typing-extensions>=4.1.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from mashumaro==3.14->boltz) (4.12.2)
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| − | Requirement already satisfied: ihm>=1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from modelcif==1.2->boltz) (1.8)
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| − | Requirement already satisfied: tqdm>=4.57.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (4.65.0)
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| − | Requirement already satisfied: fsspec>=2022.5.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (2024.12.0)
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| − | Requirement already satisfied: torchmetrics>=0.7.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (1.6.1)
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| − | Requirement already satisfied: lightning-utilities>=0.10.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (0.12.0)
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| − | Requirement already satisfied: charset-normalizer<4,>=2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.0.4)
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| − | Requirement already satisfied: idna<4,>=2.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (3.4)
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| − | Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.3.0)
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| − | Requirement already satisfied: certifi>=2017.4.17 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2024.6.2)
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| − | Requirement already satisfied: docker-pycreds>=0.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (0.4.0)
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| − | Requirement already satisfied: gitpython!=3.1.29,>=1.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.1.44)
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| − | Requirement already satisfied: platformdirs in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.10.0)
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| − | Requirement already satisfied: protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (4.25.5)
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| − | Requirement already satisfied: psutil>=5.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (5.9.0)
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| − | Requirement already satisfied: sentry-sdk>=2.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (2.20.0)
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| − | Requirement already satisfied: setproctitle in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (1.3.4)
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| − | Requirement already satisfied: setuptools in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (68.0.0)
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| − | Requirement already satisfied: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2.8.2)
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| − | Requirement already satisfied: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3.post1)
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| − | Requirement already satisfied: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3)
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| − | Requirement already satisfied: Pillow in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz) (9.4.0)
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| − | Requirement already satisfied: filelock in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.9.0)
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| − | Requirement already satisfied: networkx in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1)
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| − | Requirement already satisfied: jinja2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1.2)
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| − | Requirement already satisfied: six>=1.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz) (1.16.0)
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| − | Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (3.8.5)
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| − | Requirement already satisfied: gitdb<5,>=4.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (4.0.12)
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| − | Requirement already satisfied: msgpack in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz) (1.0.3)
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| − | Requirement already satisfied: MarkupSafe>=2.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz) (2.1.1)
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| − | Requirement already satisfied: mpmath>=0.19 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from sympy->einx==0.3.0->boltz) (1.3.0)
| |
| − | Requirement already satisfied: attrs>=17.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (22.1.0)
| |
| − | Requirement already satisfied: multidict<7.0,>=4.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (6.0.2)
| |
| − | Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (4.0.2)
| |
| − | Requirement already satisfied: yarl<2.0,>=1.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.8.1)
| |
| − | Requirement already satisfied: frozenlist>=1.1.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.3.3)
| |
| − | Requirement already satisfied: aiosignal>=1.1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz) (1.2.0)
| |
| − | Requirement already satisfied: smmap<6,>=3.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (5.0.2)
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % pip check
| |
| − | tables 3.8.0 requires blosc2, which is not installed.
| |
| − | tables 3.8.0 requires cython, which is not installed.
| |
| − | conda-repo-cli 1.0.75 requires requests-mock, which is not installed.
| |
| − | spyder 5.4.3 requires pyqt5, which is not installed.
| |
| − | spyder 5.4.3 requires pyqtwebengine, which is not installed.
| |
| − | gensim 4.3.0 requires fuzzytm, which is not installed.
| |
| − | conda-repo-cli 1.0.75 has requirement clyent==1.2.1, but you have clyent 1.2.2.
| |
| − | conda-repo-cli 1.0.75 has requirement PyYAML==6.0.1, but you have pyyaml 6.0.2.
| |
| − | conda-repo-cli 1.0.75 has requirement requests==2.31.0, but you have requests 2.32.3.
| |
| − | numba 0.57.0 has requirement numpy<1.25,>=1.21, but you have numpy 1.26.3.
| |
| − | python-lsp-black 1.2.1 has requirement black>=22.3.0, but you have black 0.0.
| |
| − | anaconda-cloud-auth 0.1.3 has requirement pydantic<2.0, but you have pydantic 2.10.6.
| |
| − | s3fs 2023.4.0 has requirement fsspec==2023.4.0, but you have fsspec 2024.12.0.
| |
| − | aiobotocore 2.5.0 has requirement botocore<1.29.77,>=1.29.76, but you have botocore 1.35.99.
| |
| − | conda-verify 3.4.2 is not supported on this platform
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % pip install boltz -U --use-deprecated=legacy-resolver
| |
| − | Requirement already up-to-date: boltz in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (0.4.1)
| |
| − | Requirement already satisfied, skipping upgrade: torch>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.2)
| |
| − | Requirement already satisfied, skipping upgrade: numpy==1.26.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.26.3)
| |
| − | Requirement already satisfied, skipping upgrade: hydra-core==1.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.3.2)
| |
| − | Requirement already satisfied, skipping upgrade: pytorch-lightning==2.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.4.0)
| |
| − | Requirement already satisfied, skipping upgrade: rdkit>=2024.3.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2024.9.4)
| |
| − | Requirement already satisfied, skipping upgrade: dm-tree==0.1.8 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.1.8)
| |
| − | Requirement already satisfied, skipping upgrade: requests==2.32.3 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.3)
| |
| − | Requirement already satisfied, skipping upgrade: pandas>=2.2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.2.3)
| |
| − | Requirement already satisfied, skipping upgrade: types-requests in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (2.32.0.20241016)
| |
| − | Requirement already satisfied, skipping upgrade: einops==0.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.8.0)
| |
| − | Requirement already satisfied, skipping upgrade: einx==0.3.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.3.0)
| |
| − | Requirement already satisfied, skipping upgrade: fairscale==0.4.13 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.4.13)
| |
| − | Requirement already satisfied, skipping upgrade: mashumaro==3.14 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (3.14)
| |
| − | Requirement already satisfied, skipping upgrade: modelcif==1.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.2)
| |
| − | Requirement already satisfied, skipping upgrade: wandb==0.18.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (0.18.7)
| |
| − | Requirement already satisfied, skipping upgrade: click==8.1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (8.1.7)
| |
| − | Requirement already satisfied, skipping upgrade: pyyaml==6.0.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (6.0.2)
| |
| − | Requirement already satisfied, skipping upgrade: biopython==1.84 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.84)
| |
| − | Requirement already satisfied, skipping upgrade: scipy==1.13.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from boltz) (1.13.1)
| |
| − | Requirement already satisfied, skipping upgrade: filelock in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.9.0)
| |
| − | Requirement already satisfied, skipping upgrade: typing-extensions>=4.8.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (4.12.2)
| |
| − | Requirement already satisfied, skipping upgrade: sympy in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (1.11.1)
| |
| − | Requirement already satisfied, skipping upgrade: networkx in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1)
| |
| − | Requirement already satisfied, skipping upgrade: jinja2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (3.1.2)
| |
| − | Requirement already satisfied, skipping upgrade: fsspec in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from torch>=2.2->boltz) (2024.12.0)
| |
| − | Requirement already satisfied, skipping upgrade: omegaconf<2.4,>=2.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (2.3.0)
| |
| − | Requirement already satisfied, skipping upgrade: antlr4-python3-runtime==4.9.* in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (4.9.3)
| |
| − | Requirement already satisfied, skipping upgrade: packaging in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz) (23.1)
| |
| − | Requirement already satisfied, skipping upgrade: tqdm>=4.57.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (4.65.0)
| |
| − | Requirement already satisfied, skipping upgrade: torchmetrics>=0.7.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (1.6.1)
| |
| − | Requirement already satisfied, skipping upgrade: lightning-utilities>=0.10.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pytorch-lightning==2.4.0->boltz) (0.12.0)
| |
| − | Requirement already satisfied, skipping upgrade: Pillow in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz) (9.4.0)
| |
| − | Requirement already satisfied, skipping upgrade: charset-normalizer<4,>=2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.0.4)
| |
| − | Requirement already satisfied, skipping upgrade: idna<4,>=2.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (3.4)
| |
| − | Requirement already satisfied, skipping upgrade: urllib3<3,>=1.21.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2.3.0)
| |
| − | Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from requests==2.32.3->boltz) (2024.6.2)
| |
| − | Requirement already satisfied, skipping upgrade: python-dateutil>=2.8.2 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2.8.2)
| |
| − | Requirement already satisfied, skipping upgrade: pytz>=2020.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3.post1)
| |
| − | Requirement already satisfied, skipping upgrade: tzdata>=2022.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from pandas>=2.2.2->boltz) (2023.3)
| |
| − | Requirement already satisfied, skipping upgrade: frozendict in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from einx==0.3.0->boltz) (2.4.6)
| |
| − | Requirement already satisfied, skipping upgrade: ihm>=1.7 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from modelcif==1.2->boltz) (1.8)
| |
| − | Requirement already satisfied, skipping upgrade: docker-pycreds>=0.4.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (0.4.0)
| |
| − | Requirement already satisfied, skipping upgrade: gitpython!=3.1.29,>=1.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.1.44)
| |
| − | Requirement already satisfied, skipping upgrade: platformdirs in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (3.10.0)
| |
| − | Requirement already satisfied, skipping upgrade: protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0; sys_platform != "linux" in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (4.25.5)
| |
| − | Requirement already satisfied, skipping upgrade: psutil>=5.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (5.9.0)
| |
| − | Requirement already satisfied, skipping upgrade: sentry-sdk>=2.0.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (2.20.0)
| |
| − | Requirement already satisfied, skipping upgrade: setproctitle in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (1.3.4)
| |
| − | Requirement already satisfied, skipping upgrade: setuptools in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from wandb==0.18.7->boltz) (68.0.0)
| |
| − | Requirement already satisfied, skipping upgrade: mpmath>=0.19 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from sympy->torch>=2.2->boltz) (1.3.0)
| |
| − | Requirement already satisfied, skipping upgrade: MarkupSafe>=2.0 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz) (2.1.1)
| |
| − | Requirement already satisfied, skipping upgrade: six>=1.5 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas>=2.2.2->boltz) (1.16.0)
| |
| − | Requirement already satisfied, skipping upgrade: msgpack in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz) (1.0.3)
| |
| − | Requirement already satisfied, skipping upgrade: gitdb<5,>=4.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (4.0.12)
| |
| − | Requirement already satisfied, skipping upgrade: smmap<6,>=3.0.1 in /Users/supremestudier/anaconda3/lib/python3.11/site-packages (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz) (5.0.2)
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % conda activate
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % conda env list
| |
| − | # conda environments:
| |
| − | #
| |
| − | base * /Users/supremestudier/anaconda3
| |
| − | sage-dev /Users/supremestudier/anaconda3/envs/sage-dev
| |
| − | /Users/supremestudier/opt/anaconda3
| |
| − |
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % which boltz
| |
| − | /Users/supremestudier/anaconda3/bin/boltz
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ home
| |
| − | (base) [ehspector@milan1 espector]$ cd 4s0v/
| |
| − | (base) [ehspector@milan1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@milan1 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@milan1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ cd no_charge/
| |
| − | (base) [ehspector@milan1 no_charge]$ ls
| |
| − | 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in
| |
| − | 4s0v.lig_no_charge.min_scored.mol2 gas_2.out
| |
| − | 4s0v_no_hydrogens_no_charges.mol2 gas.out_scored.mol2
| |
| − | (base) [ehspector@milan1 no_charge]$ vi 4s0v_ligand_hydrogens_no_charges.mol2
| |
| − | (base) [ehspector@milan1 no_charge]$ ls
| |
| − | 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in
| |
| − | 4s0v.lig_no_charge.min_scored.mol2 gas_2.out
| |
| − | 4s0v_no_hydrogens_no_charges.mol2 gas.out_scored.mol2
| |
| − | (base) [ehspector@milan1 no_charge]$ cd ..
| |
| − | (base) [ehspector@milan1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@milan1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@milan1 4s0v]$ cd energy_min/
| |
| − | (base) [ehspector@milan1 energy_min]$ ls
| |
| − | 4s0v.lig.min_scored.mol2 min.in min.out
| |
| − | (base) [ehspector@milan1 energy_min]$ vi 4s0v.lig.min_scored.mol2
| |
| − | (base) [ehspector@milan1 energy_min]$ cd ..
| |
| − | (base) [ehspector@milan1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@milan1 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@milan1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas.out_scored.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ cd no_charge/
| |
| − | (base) [ehspector@milan1 no_charge]$ ls
| |
| − | 4s0v_ligand_hydrogens_no_charges.mol2 gas_2.in
| |
| − | 4s0v.lig_no_charge.min_scored.mol2 gas_2.out
| |
| − | 4s0v_no_hydrogens_no_charges.mol2 gas.out_scored.mol2
| |
| − | (base) [ehspector@milan1 no_charge]$ vi 4s0v_ligand_hydrogens_no_charges.mol2
| |
| − | (base) [ehspector@milan1 no_charge]$ cd ..
| |
| − | (base) [ehspector@milan1 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@milan1 4s0v]$ vi energy_min/4s0v.lig.min_scored.mol2
| |
| − | (base) [ehspector@milan1 4s0v]$ cp energy_min/4s0v.lig.min_scored.mol2 gas_teiger/test.mol2
| |
| − | (base) [ehspector@milan1 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@milan1 gas_teiger]$ ls
| |
| − | gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas.out no_charge no_gas.out test.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi test.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi test.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ cp gas.in gas_2.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ pwd
| |
| − | /gpfs/projects/rizzo/espector/4s0v/gas_teiger
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ ls
| |
| − | gas_2.in gas.in gas.out_scored.mol2 no_gas.in no_gas.out_scored.mol2
| |
| − | gas_2.out gas.out no_charge no_gas.out test.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_2.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ home
| |
| − | (base) [ehspector@milan2 espector]$ cd 4s0v/gas_teiger/
| |
| − | (base) [ehspector@milan2 gas_teiger]$ ls
| |
| − | gas_2.in gas.out no_gas.in test.mol2
| |
| − | gas_2.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2
| |
| − | gas.in no_charge no_gas.out_scored.mol2
| |
| − | (base) [ehspector@milan2 gas_teiger]$ vi gas_2.in
| |
| − | (base) [ehspector@milan2 gas_teiger]$ cp gas_2.in gas_3.in
| |
| − | (base) [ehspector@milan2 gas_teiger]$ vi gas_3.in
| |
| − | (base) [ehspector@milan2 gas_teiger]$ dock6 -i gas_3.in -o gas_3.out
| |
| − | (base) [ehspector@milan2 gas_teiger]$ ls
| |
| − | gas_2.in gas_3.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2
| |
| − | gas_2.out gas.in no_charge no_gas.out_scored.mol2
| |
| − | gas_3.in gas.out no_gas.in test.mol2
| |
| − | (base) [ehspector@milan2 gas_teiger]$ vi gas_3.out
| |
| − | (base) [ehspector@milan2 gas_teiger]$ vi gas_3.in
| |
| − | (base) [ehspector@milan2 gas_teiger]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ ls
| |
| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@milan2 ~]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | 1086 5EEN class_project class_work
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd class_
| |
| − | -bash: cd: class_: No such file or directory
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd class_work/
| |
| − | (base) [ehspector@milan2 class_work]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 class_work]$ cd ..
| |
| − | (base) [ehspector@milan2 AMS_536]$ mkdir Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ mv class_work/ Tutorials/
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | 1086 5EEN class_project Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | class_work
| |
| − | (base) [ehspector@milan2 Tutorials]$ mv class_work/ 2w26
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 2w26
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan2 AMS_536]$ mv 1086/ 5EEN/ Tutorials/
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1086 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 2w26]$ cd 001
| |
| − | -bash: cd: 001: No such file or directory
| |
| − | (base) [ehspector@milan2 2w26]$ cd 001_structure/
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | 2w26_ligand_hydrogens_charges.mol2 2w26_protein_no_hydrogens_no_charges.mol2
| |
| − | 2w26_ligand_no_hydrogens_no_charges.mol2 2w26_protein_with_charges.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ rm *.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | (base) [ehspector@milan2 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26_new_surface.dms 2w26.sph INSPH OUTSPH selected_spheres.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ rm selected_spheres.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ rm 2w26.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ rm 2w26_new_surface.dms
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | INSPH OUTSPH sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | INSPH sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 01showbox.sh 2w26.box.pdb grid.in grid.out grid.sh showbox.in '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ rm 2w26.box.pdb
| |
| − | (base) [ehspector@milan2 003_gridbox]$ rm grid.out
| |
| − | (base) [ehspector@milan2 003_gridbox]$ mv 01showbox.sh showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | grid.in grid.sh showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 2w26]$ cd 004_dock/
| |
| − | (base) [ehspector@milan2 004_dock]$ ls
| |
| − | (base) [ehspector@milan2 004_dock]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 2w26/commands.txt 5EEN/commands.txt
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 5EEN/
| |
| − | (base) [ehspector@milan2 5EEN]$ ls
| |
| − | commands.txt
| |
| − | (base) [ehspector@milan2 5EEN]$ bash commands.txt
| |
| − | (base) [ehspector@milan2 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan2 5EEN]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/001_structure/
| |
| − | (base) [ehspector@milan1 001_structure]$ pwd
| |
| − | /gpfs/home/ehspector/AMS_536/Tutorials/5EEN/001_structure
| |
| − | (base) [ehspector@milan1 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 001_structure/
| |
| − | (base) [ehspector@milan1 001_structure]$ ls
| |
| − | 5een_H_cH.mol2 5een_ligand_H_cH.mol2 5een_ligand_noH_nocH.mol2 5een_noH_nocH.mol2
| |
| − | (base) [ehspector@milan1 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 5een_surface.dms
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | INSPH sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/002_surface_spheres/sphere.sph 5EEN/002_surface_spheres/sphere.sph
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 5EEN/002_surface_spheres/
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 5een_surface.dms INSPH sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ vi sphere.sph
| |
| − |
| |
| − |
| |
| − | Press ENTER or type command to continue
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ bash sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 5een.sph 5een_surface.dms INSPH OUTSPH sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ vi OUTSPH
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 5een.sph 5een_surface.dms INSPH OUTSPH sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan1 2w26]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | INSPH sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ vi sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 5EEN/002_surface_spheres/
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 5een.sph 5een_surface.dms INSPH OUTSPH sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ vi selected_sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 001_structure/
| |
| − | (base) [ehspector@milan1 001_structure]$ ls
| |
| − | 5een_H_cH.mol2 5een_ligand_H_cH.mol2 5een_ligand_noH_nocH.mol2 5een_noH_nocH.mol2
| |
| − | (base) [ehspector@milan1 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ vi selected_sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ bash selected_sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 5een.sph INSPH selected_sphere.sph sphere.sph
| |
| − | 5een_surface.dms OUTSPH selected_spheres.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ mv selected_sphere.sph select.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ vi selected_spheres.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan1 5EEN]$ mv 004_dock/ 004_energymin
| |
| − | (base) [ehspector@milan1 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan1 003_gridbox]$ vi showbox.in
| |
| − | (base) [ehspector@milan1 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/
| |
| − | (base) [ehspector@milan1 003_gridbox]$ ls
| |
| − | grid.in grid.sh showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/showbox.sh 5EEN/003_gridbox/showbox.sh
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 5EEN/
| |
| − | (base) [ehspector@milan1 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan1 003_gridbox]$ ls
| |
| − | showbox.in showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ vi showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ bash showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ ls
| |
| − | 5een.box.pdb showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan1 003_gridbox]$ ls
| |
| − | 5een.box.pdb grid.in showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ rm grid.in
| |
| − | (base) [ehspector@milan1 003_gridbox]$ ls
| |
| − | 5een.box.pdb showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/
| |
| − | (base) [ehspector@milan1 003_gridbox]$ ls
| |
| − | grid.in grid.sh showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan1 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/grid.in 5EEN/003_gridbox/grid.in
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/003_gridbox/grid.sh 5EEN/003_gridbox/grid.sh
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 5EEN/003_gridbox/
| |
| − | (base) [ehspector@milan1 003_gridbox]$ ls
| |
| − | 5een.box.pdb grid.in grid.sh showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 001_structure/
| |
| − | (base) [ehspector@milan1 001_structure]$ ls
| |
| − | 5een_H_cH.mol2 5een_ligand_H_cH.mol2 5een_ligand_noH_nocH.mol2 5een_noH_nocH.mol2
| |
| − | (base) [ehspector@milan1 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan1 003_gridbox]$ ls
| |
| − | 5een.box.pdb grid.in grid.sh showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ vi grid.
| |
| − | (base) [ehspector@milan1 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan1 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan1 003_gridbox]$ ls
| |
| − | 5een.box.pdb grid.in grid.sh showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/003_gridbox/
| |
| − | (base) [ehspector@milan1 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan1 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 5EEN/003_gridbox/
| |
| − | (base) [ehspector@milan1 003_gridbox]$ ls
| |
| − | 5een.box.pdb grid.in grid.sh showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ vi grid.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ bash grid.sh
| |
| − | (base) [ehspector@milan1 003_gridbox]$ ls
| |
| − | 5een.box.pdb grid.in grid.out showbox.in showbox.sh
| |
| − | grid.bmp grid.nrg grid.sh '&showbox.log&'
| |
| − | (base) [ehspector@milan1 003_gridbox]$ vi grid.out
| |
| − | (base) [ehspector@milan1 003_gridbox]$ cd ../004_energymin/
| |
| − | (base) [ehspector@milan1 004_energymin]$ ls
| |
| − | (base) [ehspector@milan1 004_energymin]$ touch min.in
| |
| − | (base) [ehspector@milan1 004_energymin]$ ls
| |
| − | min.in
| |
| − | (base) [ehspector@milan1 004_energymin]$ dock6 -i min.in
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released April 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
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| − |
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| − |
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| − | Conformational Sampling Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
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| − |
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| − | Internal Energy Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | use_internal_energy [yes] (yes no):yes
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| − | internal_energy_rep_exp [12] ():
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| − | internal_energy_cutoff [100.0] ():
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| − | Note: Internal energy only includes repulsive VDW for growth and/or minimization.
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| − |
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| − | Molecule Library Input Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | ligand_atom_file [database.mol2] ():../001_structure/5een_ligand_H_cH.mol2
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| − | limit_max_ligands [no] (yes no):
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| − | skip_molecule [no] (yes no):
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| − | read_mol_solvation [no] (yes no):
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| − | calculate_rmsd [no] (yes no):yes
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| − | use_rmsd_reference_mol [no] (yes no):yes
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| − | rmsd_reference_filename [ligand_rmsd.mol2] ():../001_structure/5een_ligand_H_cH.mol2
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| − |
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| − | Database Filter Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | use_database_filter [no] (yes no):no
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| − |
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| − | Orient Ligand Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | orient_ligand [yes] (yes no):no
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| − |
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| − | Bump Filter Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | bump_filter [no] (yes no):no
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| − |
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| − | Master Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | score_molecules [yes] (yes no):yes
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| − |
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| − | Contact Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | contact_score_primary [no] (yes no):
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| − |
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| − | Grid Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | grid_score_primary [yes] (yes no):
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| − | grid_score_rep_rad_scale [1] ():
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| − | grid_score_vdw_scale [1] ():
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| − | grid_score_es_scale [1] ():
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| − | grid_lig_efficiency [no] (yes no):
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| − | grid_score_grid_prefix [grid] ():../003_gridbox/grid
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| − | GIST Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | MultiGrid Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | Dock3.5 Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | Continuous Energy Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | Footprint Similarity Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | Pharmacophore Similarity Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | Hbond Energy Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | Internal Energy Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | Descriptor Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | Zou GB/SA Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | Hawkins GB/SA Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | SASA Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | Amber Score Parameters
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − | Simplex Minimization Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | minimize_ligand [yes] (yes no):
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| − | simplex_max_iterations [1000] ():
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| − | simplex_tors_premin_iterations [0] ():
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| − | simplex_max_cycles [1] ():
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| − | simplex_score_converge [0.1] ():
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| − | simplex_cycle_converge [1.0] ():
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| − | simplex_trans_step [1.0] ():
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| − | simplex_rot_step [0.1] ():
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| − | simplex_tors_step [10.0] ():
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| − | simplex_final_min [no] (yes no):
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| − | simplex_random_seed [0] ():
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| − | simplex_restraint_min [no] (yes no):yes
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| − | simplex_coefficient_restraint [10.0] ():
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| − |
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| − | Atom Typing Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | atom_model [all] (all | united):
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| − | vdw_defn_file [vdw.defn] ():defn
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| − | flex_defn_file [flex.defn] ():defn
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| − | flex_drive_file [flex_drive.tbl] ():defn
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| − |
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| − | Molecule Library Output Parameters
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| − | ------------------------------------------------------------------------------------------
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| − | ligand_outfile_prefix [output] ():5een.lig.min
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| − | write_mol_solvation [no] (yes no):
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| − | write_orientations [no] (yes no):
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| − | num_scored_conformers [1] ():
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| − | score_threshold [100.0] ():
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| − | rank_ligands [no] (yes no):
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| − | ------------------------------------------------------------------------------------------
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| − |
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| − |
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| − | Could not open defn for reading. Program will terminate.
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| − |
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| − | (base) [ehspector@milan1 004_energymin]$ ls
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| − | min.in
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| − | (base) [ehspector@milan1 004_energymin]$ vi min.in
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| − | (base) [ehspector@milan1 004_energymin]$ cd ../../
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| − | (base) [ehspector@milan1 Tutorials]$ cd ../../
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| − | (base) [ehspector@milan1 ~]$ ls
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| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
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| − | (base) [ehspector@milan1 ~]$ cd
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| − | (base) [ehspector@milan1 ~]$ ls
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| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
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| − | (base) [ehspector@milan1 ~]$ cd ..
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| − | (base) [ehspector@milan1 home]$ ls
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| − | cd ..aaachase dbluestein jkottmann msavenkov skomatireddy
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| − | aaaggarwal dbobo jksullivan msayana skoppuravuri
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| − | aaaggarwal.26FEB2020 dcalabria jktsui msazonova skorada
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| − | aabdurrob dcazorla jleehand mschedel skotelnikov
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| − | aabhilash dcbrown jlfong mschrimpf skotla
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| − | aadarsh dcharan jlguerra mschwaller skrichevsky
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| − | aadubois dchien jlipshultz mshaaban skristam
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| − | aagashe ddassanis jlomanto mshahneousba skrupp
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| − | aagishtein ddelayo jluceno mshih sladerwager
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| − | aahern ddemartini jlungu mshinder slakshminara
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| − | aaiyer ddukes jlutsky mshu slaverty
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| − | aajith deachen jlweissman msilfies slthomas
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| − | aakale decarlson jmaghakian msmoawad smadishetty
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| − | aakiti dekblom jmarcantonio msrao smaiti
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| − | aakkumar delam jmarciano msreeves smallipattu
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| − | aaksenova demccabe jmayortorres mstanacevic smamalis
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| − | aaliang dereliu jmeliker msweber smartynenko
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| − | aallin deroy jmendezmende mtalukder smascarenhas
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| − | aallu devlin jmgentile mthu smconnors
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| − | aalpern dfarahmandpo jmiao mtoledorozyc smdick
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| − | aamahmood dfei jmitchell mtsonev smedved
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| − | aambrown dfucich jmorkos mturk smeghdadizan
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| − | aamgalan dgaidhani jmulackal mumarani smelhiraj
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| − | aaminev dgenet jmurrugarral muprit smesiha
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| − | aamurthy dgersappe jmurzaku mvalakonda smhenry
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| − | aanaggarwal dg-mgmt1-auth-keys jmvasquez mvashishtha smiduthuri
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| − | aanagnostopo dg-mgmt2-auth-keys jnassar mvfernandezs smilakovic
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| − | aanik dgnatenko jnatarajan mvilensky smirghafouri
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| − | aaprasad dgoon jnery mwilking smirroshande
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| − | aarasappan dgruzdev jnicasio myarif smofakham
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| − | aarefin dgursoy jnmauro myearsley smui
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| − | aarmas dgwood jnong myoungblood smukherjee
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| − | aarroyave dhailegeorgi joawilson mysql smvaccaro
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| − | aasim dhamam jocai mzamani snarmeen
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| − | aaslov dhandzlik jocwilliams mzepedaaguil snigam
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| − | aates dhdesouza jodey mzhang snikhil
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| − | aaurora dhildreth jodoh naahassan snimatullo
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| − | aavadhani dhongyi jodweinstein nabchowdhury snizambad
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| − | aavira dhperumal joeleung nabsyed snolas
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| − | aaydin dhualong joeychan nacchen snyman
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| − | aaysheth diannace jofranklin nacharya soba
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| − | ababbar disandovalch johbernard nagnihotri sochakrabort
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| − | abadhe diwliu johnliu nagutierrez sohshin
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| − | abahadori djagnarain joifan nalewis sohtsuka
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| − | abaidya djgold jomyoung nanqwang solhapark
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| − | aball djlambert jonamartins napopova somishra
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| − | abardizbania djoh jonicholson naqiu somunoz
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| − | abbhaskar djulian jonsu nasweet sooapark
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| − | abeahmad djyu jonyin natsai sopjang
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| − | abenslama dkadams joolee nazzhou sortizbetanc
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| − | abialkowska dkharzeev joosuh nbalasubrama sosarangi
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| − | abjoshi dkirby joroiland nbasok sosuresh
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| − | abkanevsky dkozakov joshmathew nbayas sowu
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| − | abogetti dkunjadiya joshumartin nbodduluri sozturk
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| − | aborad dlanger jovvazquezri nbosviel spaci
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| − | aborcatasciu dlhe joying nbowers spandrekar
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| − | aborger dlucksted jozhao nciotoli spang
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| − | aborowicz dmahalli jpantano ncmeloottu spapazahario
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| − | abozin dmahzabin jparise ncpathak spapazis
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| − | abphilip dmale jparkinson ndcertain sparvathredd
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| − | abrady dmarkov jpascal ndev spathrose
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| − | absalem dmarr jpcastillo ndheilly spilkey
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| − | abtambe dmckinnon jperezrios ndigrandi spiret
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| − | aburford dmirfenderes jpeshansky ndnguyen splee
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| − | acage dmorenosanti jpitt ndokania spochron
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| − | acalder dmukherjee jpmoryl ndurand spothumahant
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| − | acali dmulbagalven jporavanthat ndzikowski spriyadarsha
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| − | acamino dnanjappa jpwhite nesteves spugach
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| − | acastiblanco dnimatullo jqxiao nexposescan sqavi
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| − | accapua dnterry jranjan neyang srahmani
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| − | acchakravart dobyrne jrawski nezheng sraisinghani
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| − | acherath dochoi jrcheung nfaiza sramanarajan
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| − | achouhan dofu jrcorbett nfpugliese sramanarajan.OLD
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| − | acmarra dohhlee jrest nganu sramjan
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| − | adamare dokkang jrgorman nghoang sramstrom
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| − | adanial dongsong jrimel ngitman srashidian
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| − | adanoji dongwhan jrkamler ngluck sretineni
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| − | adharan donshi jrleeman ngujarati srgupte
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| − | adiloreto dotan jrojahn nhamdan srnalluri
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| − | ading doyjang jrutledge nhirtle srpayne
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| − | admannino dozhong jrwei nichaturvedi srshende
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| − | adpeng dpadhorny jsaldivar nidimeglio ssabaghian
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| − | adpollack dpare jsalley nigreen ssagynbayeva
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| − | adrana dparedesmeri jsaltz nileong ssandal
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| − | adrflorio dparwana jsaputo niranmanesh ssarnot
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| − | adrogers dpati jsaxena nisankar ssarwar
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| − | adubey dpatil jscanderson nisong sseepersaud
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| − | adutt dpenchoff jschuchart nisoni ssemerkant
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| − | aecuomo dpfennell jschwedes nivsingh sserbin
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| − | aeichert dpotemkin jseeliger njschwartzap sshaharia
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| − | aeltareb drendina jseol nkahmed sshapourmian
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| − | aeweiss drhamilton jsgordon nkandru ssheikhi
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| − | afahmed dschneble jsinanan nkatla sshoque
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| − | afarhadzadeh dseddoh jsistla nkdean sshrestha
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| − | afgregory dsforza jskowalski nkeer sshrivastava
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| − | afrigo dshangase jslogan nkhalsa ssivalenka
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| − | afurey dsingla jsmaers nkhandagale ssjohn
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| − | agaffoor dsli jsmucker nkhatri sskiena
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| − | agaikwad dslo jsteier nkinalis ssomani
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| − | agarforth dsmolarski jsuchan nkinlock ssperrottet
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| − | agargueta dstepanenko jtalaveragre nkyose sstoller
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| − | agauer dstrenski jtekverk nleak sstoyanov
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| − | aghai dswesty jtepan nlogozzo ssundar
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| − | agilgomez dthanassi jtevans nlrogers ssunia
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| − | agmaharaj dtpham jtgabrielli nmahamud ssyedfahad
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| − | agnsinha dtsybychev jtjones nmaher ssyritsyn
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| − | agopalkrishn dtung jtmessina nmanzella staralekar
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| − | agraikos duwwang jtrelewicz nmarcella stawong
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| − | agugel dvahabli jtrue nmathew stelehany
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| − | agulhane dvyas juaalcantara nmehanna sthaker
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| − | ahsingh dziadlou junding nmichielsen stomar
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| − | aicheng eatkinson junhuzhang nnaitlho ststern
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| − | ailyu ebartlett junjiang nnawal stzeng
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| − | ajamieson ebrini junwang5 noibrahim sunarasimhas
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| − | ajasniew ebryski junxialiu nolconner sunarasimhas.OLD
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| − | ajchan ecarcelespov junywang novsingh sunghucho
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| − | ajchavez ecgross jusandoval npahlavan sunkim2
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| − | ajhong echurch juschan npanagodawet surmy
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| − | ajkoller eclemmon jusliu nparghi sushahid
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| − | ajoung ecowley jusu npomata svaldez
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| − | ajwelsh edowney juzou nramdin svee
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| − | ajyadav edzhang jvansnellenb nreaton swaxman
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| − | akalugade eeryildiz jvaska nsalekfarama swchaudhury
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| − | akanodia efinson jverbaarscho nsampson swen
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| − | akapote egebb jvishal nsehgal sweverma
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| − | akarkare egentles jvpepe nshouman swpaul
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| − | akarzai egouvis jvu nsimakov sxchen
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| − | akaufman eheywood jwahhab nsipperly syaddanapudi
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| − | akhibovska ehspector jwcross nsmehta syalla
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| − | akhosronejad ejcarey jwcusick nsoder syarma
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| − | akhoukhi ejguan jwisdom nsokolow syatigala
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| − | akingan ejli jwlodek nsomani syatskar
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| − | akirillov ejohnfelt jxue nstreb sydiaz
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| − | akkale ekandov jyerrick ntadler syousef
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| − | akonosky ekbetancourt jyluo ntardugno sytlee
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| − | akravchuk ekeck jzoodsma ntetrault tabhatia
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| − | akrowe ekeough kabichandani ntippabhatla tadoyle
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| − | aktyagi ekhew kadeng ntripti taeklee
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| − | akucich eklau kadiallo nvafaeinajaf taeyounkim
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| − | akuduregundi ekoo kadill nvitek tagiles
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| − | akundhuru elari kadreher nvohra tahkhan
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| − | akverma elettieri kafarber nvsutherland tajjung
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| − | akwakye elgchan kaifzheng nwein takther
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| − | alabella elharris kaili nwweber talama
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| − | alaing eli kailiu2 nxlee talare
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| − | alanhuang ellai kailjiang nyfletcher talin
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| − | alchung elleisenberg kaimxu obellinson tallison
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| − | aldong elmlowe kaitong odeshpande tamislam
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| − | aldraper elogeswar kaixichen odiamond tanis
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| − | alehsu elslattery kamhassan odickerson taryu
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| − | alem emacosta kamrivera oeskiocak tbabu
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| − | alexhernande emarants kanagarwal ohaputhanthr tbertino
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| − | alfwu emarkowitz kanzhao ohyejin tbrackins
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| − | algrullon emarzigliano kapatel okim tbrinckmann
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| − | alhhuang embriggs kaporter okoren tbrinkley
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| − | alianwar emrlin kapu omcgranaghan tburfeind
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| − | alicwang emroberts karamachandr omorozova tbushra
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| − | alietzau emyhand kargill omoy tcanli
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| − | alifeng enebet kasong onatu tchatterton
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| − | aliguori eoruro katalwar oogunfolakan tchristy
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| − | allekim epapadopoulo kbaylous orambow tcotroneo
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| − | allelin erandhawa kbdiaz osdeshpande tdawar
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| − | allwong eraut kbeckerredd oshakkour tdiprima
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| − | almabraham erbraun kbelfon oshetty tdviri
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| − | almishra erfan kberard osteele tema
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| − | alokre erglukhov kberghaus oyang testro
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| − | alowell ericlin1 kccoughlin oyasar tgavryshko
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| − | alperezmendo erizhou kchetan padari tglotch
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| − | alqin erkumar kchitale paggarwal tgrgas
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| − | alsli erluo kdas pahan tgrossberndt
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| − | alvhsu erosenberg kdavidson pallen tguttula
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| − | alynegron errjones kdehmelt pamishra thamada
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| − | amacinnis erschroeder kdemir parjain thausch
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| − | amaffei erwhuang kdevedzhiev parmitage thdavidson
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| − | amanagarwal esahin kdhar patflanagan therault
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| − | amanpsingh esalman kdhuri patmuller therodrigues
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| − | amanzoor esaraivanov kdyro pavkirkar thollis
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| − | amaresca eschiltzrous kebui pavnkaur thomlin
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| − | amarya eshaji keckartt pawu thren
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| − | amassari eshetreatkle kelam payao thzhou
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| − | amasuno eshih keliao pb tianyuawang
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| − | ambbrown eshuryak kellywang pbaliga tili
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| − | amccumber esicoli kelvlin pcascantebon timji
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| − | amcelroy esiegmann kenchin pcastillo timshi
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| − | amchale esogut kenhu pchinthamred tinggao
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| − | amcpherran esonmez kennwu pdalaya tinghwu
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| − | amehla essingh kereid pdamore tingliu2
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| − | amehmood eswong kerwood pdevarajan tingslin
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| − | amgondal etakeuchi kevazquez pdjuric tinliu
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| − | amibrahim etalis kevcai pdonat tiwwong
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| − | amigues etchan kevcheng pdongle tixi
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| − | amisaha etcheung keviliu pdutta tiyuan
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| − | amkgupta ethresher kevwei pechang tjarrett
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| − | amnoonan etmonaco kexi peihsieh tjohannessen
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| − | amohamed etrommer kfatema peinwang tkarwal
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| − | amohammadrez etsang kfernando penzhang tknoll
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| − | amohanty etwest kflora pesun tkohlmann
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| − | amohideen etyen kfryer pferrero tkral
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| − | amoonilal evalin kgarg pgaikar tkurc
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| − | amrabet evaxie kgayadhankar pganapathi tla
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| − | amramroop evergaracobo kgcassar pganesh tlata
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| − | amrangwala evxie kgjonas pgodoy tloden
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| − | amritpsingh ewpeterson kgoranta pgoldbart tlonsway
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| − | amullhaupt exiu kgulati pgoriparthi tmcgee
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| − | amychen5 eylei khajny pgubbala tmia
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| − | amyla eyzhu khasegawa pguo tmohandas
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| − | anadelgado fabdinov khoh pgurung tmoriya
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| − | analekseenko faliang khumphries phariprasad tmsmyth
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| − | anarora falmodaresit khyunjae phowlader tmuntean
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| − | chanzhang jasjiang mghogale sbinnamangal yoshen
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| − | charwong jasolau mgholamianji sbire youcha
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| − | chccai jasonwang mgivehki sbirrer youngkwon
| |
| − | chdang jaswsingh mgwhite sboddeti younkang
| |
| − | chen110 jathoffman mhanubal sboppudi yousshin
| |
| − | chen147 jaygutierrez mhare sbrahmadevar ypichkar
| |
| − | chen15 jazpurua mhaziz sbscott yrhamatzada
| |
| − | chen157 jbak mhijikata sburgert ysingh
| |
| − | chen175 jbakalis mhorowitz scberg ysoh
| |
| − | chen181 jbalsamo mhott scduppala yson
| |
| − | chen182 jbarrantes miachristie scentorrino ysoroka
| |
| − | chen32 jbarron miahe schheda ytham
| |
| − | chen77 jbernauer mianchen schiappone yuanjchen
| |
| − | chencjiang jbeutel mibbowman schook yuanzhao
| |
| − | chenclu jbhambure michaliang scokro yuasong
| |
| − | chenczhu jbickel michelhuang scsteiger yuchen4
| |
| − | chenghli jbkelly michellhuang sdedhia yuchen7
| |
| − | chengklin jbohne michhuang sdefaz yuchzhou
| |
| − | chengpsun jbraick micnicolette sdescalso yucma
| |
| − | chenliang jbrimlow micxu sdhalleweyn yucpu
| |
| − | chetheringto jbrunelle miczhao sdisalvo yucsun
| |
| − | cheye jbuckley miduan sdivilov yucxing
| |
| − | chezheng jbuckley.OLD mignatov sdsouza yucye
| |
| − | chgraham jburzachiell mihur sdssingh yudding
| |
| − | chguo jcano mijia sebramirezvi yudichen
| |
| − | chhhogan jcaputi mijrivera seg yuechen4
| |
| − | chichiang jcassella milobi seojchang yuefandeng
| |
| − | chienlee jcespedes miloska seongan yuehuang
| |
| − | chihhchang jchaillet mimak seonghjeong yuejin
| |
| − | chihu jchivu minghazhang seongioh yuewang6
| |
| − | chiuyu jchlee mingsun seshin yuewang7
| |
| − | chlow jcmichel mingyli sestoller yuewlin
| |
| − | chmorales jcodere mingyzhang seunchoi yuezhao2
| |
| − | chodgdon jcolaizzo minhwang sexia yufchen
| |
| − | chou jcollier minkwan sfardeen yuhajiang
| |
| − | chriskim jconesa miray sfarhat yuhwu
| |
| − | christwong jdarling mireza sfarnan yulma
| |
| − | chtian jdcraig miswong sfinch yuluwang
| |
| − | chuahuang jdeneau mjadhav sfiola yulyu
| |
| − | chugo jdesilva mjavanmard sfluo yumichen
| |
| − | chuntchan jdovi mjbonney sgajjala yunhxu
| |
| − | chuzhu jdscully mjchun sgala yunjeon
| |
| − | chuzou jdubnau mkaltak sgenovese yunlzhang
| |
| − | chyou jdwarren mkamiya sghavamnia yunpan
| |
| − | chyyoon jecao mkanasani sghavat yupeng
| |
| − | chzuo jefzhong mkanasani.OLD sgholami yuqianwu
| |
| − | cikang jegaillard mkapadia sghorashi yuqiao
| |
| − | ciriccio jejchan mkaribian sgopalan yushuang
| |
| − | cjbyrnes jelau mkhemchandan sgoswami yusjin
| |
| − | cjzheng jelsoudy mkishore sgrao yuttian
| |
| − | ckapre jemak mkochert sgrieninger yuwang7
| |
| − | ckarwan jemchen mkoga sgurram yuwzhang
| |
| − | ckelton jenfu mkondeti sguru yuxia4
| |
| − | ckochath jepace mkonovalyuk sgwilliams yuxlin
| |
| − | cksullivan jerlin mkoraiem sgyuho yuxuanzhang
| |
| − | cleeliang jeryeung mkpatel shaamin yuxushi
| |
| − | clegett jesgoldstein mkritzer shakislam yuxwu
| |
| − | clfischer jeslong mksanda shalirou yuyguo
| |
| − | clongarini jessewang mkurakula shanhe yuzhwang
| |
| − | clsears jettran mlaul shanlin2 yyokoi
| |
| − | cltong jevalle mlauterbur shaoliu zafahmad
| |
| − | cltucker jeyeung mlcollier shaowang zalseika
| |
| − | cluhmann jeyyoo mlng shaqin zariahmed
| |
| − | clwolfe jfmoon mlondoo sharinarayan zballard
| |
| − | cmack jgaige mloverde shawmathew zbhinderwala
| |
| − | cmcarey jgajello mmadeira shcchakrabor zcheslog
| |
| − | cmcgrew jgergen mmahboob shclay zcytryn
| |
| − | cmehndiratta jglazar mmahim shdesai zdoora
| |
| − | cmflynn jglimm mmaitra shdixit zdowling
| |
| − | cmfoley jgurevitch mmakeev shdixit.OLD zdupont
| |
| − | cmjurgensen jhajagos mmarder shechoi zexizhang
| |
| − | cmkennedy jharder mmaskaliova shengzhu zeyao
| |
| − | cmoczygemba jheerwig mmasoumi shengzwang zezhu
| |
| − | cmoote jheinz mmatero shenjin zfallon
| |
| − | cmorantesari jheraghty mmaung sheshao zgrandison
| |
| − | cmwoo jhjung mmcduffie shexiong zgungor
| |
| − | cnoe jhollister mmcneill shikgupta zhacai
| |
| − | cnoutsos jhpark mmerenstein shilgupta zhage
| |
| − | codlam jiabwang mmilhaven shilliu zhagu
| |
| − | cohwarner jiachzhu mmimurphy shiltian zhang100
| |
| − | cojiang jiacxu mmursheed shitsai zhang110
| |
| − | cokeoma jiahuwang mniznikiewic shivansharma zhang118
| |
| − | coleary jiajgao mnovotny shivgupta zhang123
| |
| − | concao jiaji moamin shiyuawang zhang133
| |
| − | conliu jiakwang mobusan shkhalid zhang142
| |
| − | cpercival jialai moewilliams shmmohammed zhang152
| |
| − | cpethe jialin1 moflus shmondal zhang173
| |
| − | cpinizzotto jiamili mogao shopatel zhanyang
| |
| − | cplizio jiamwu mogoel shperalta zhaoliu
| |
| − | cprasad jianfeng mohassan shrajput zhchai
| |
| − | cqiu jianflin mojia shroy zhddong
| |
| − | cradke jianhan molssi000 shrraman zhedzhang
| |
| − | crcollinswor jianjliu molssi001 shsaha zhefang
| |
| − | crfernandesv jianmtan molssi002 shshekhar zheng13
| |
| − | csangiovanni jiannyang molssi003 shshekhar.OLD zheng30
| |
| − | csantoni jianxiozhang molssi004 shsin zhengxwang
| |
| − | csasmith jiaojiang molssi005 shssridhar zhenjhuang
| |
| − | cschwaner jiapatel molssi006 shtao zhenliu
| |
| − | cshiveshwark jiasu molssi007 shuaguo zhenlu
| |
| − | csiebor jiatian molssi008 shubwang zhenqian
| |
| − | csimmerling jiawang1 molssi009 shuhe zhenwu
| |
| − | csingleton jiaweichen molssi010 shujia zhenxliu
| |
| − | cstussman jiawezhu molssi011 shyyoo zheychen
| |
| − | csyreilly jiaxuyu molssi012 shyyuan zhezhou1
| |
| − | cthakur jiayeguo molssi013 shzzhou zhibwang
| |
| − | ctinker jiayyan molssi014 siasun zhibyang
| |
| − | ctustin jibbai molssi015 sichchen zhideng
| |
| − | cuwang jichao molssi016 sicheliu zhihhe
| |
| − | cvorkas jiddong molssi017 sichhabra zhihhuang
| |
| − | cweistuch jiechen3 molssi018 sichliu zhijli
| |
| − | cwoellhof jiemchen molssi019 sigadkar zhimalin
| |
| − | cxi jiemzeng molssi020 siggupta zhipxu
| |
| − | cyanagisawa jienzhu molssi021 sihqian zhiwlin
| |
| − | cyluo jieyang molssi022 sijhuang zhixzhang
| |
| − | cyoungflesh jihlin molssi023 sijjiang zhiye
| |
| − | czhen jihoopark molssi024 sijliu zhke
| |
| − | d9wang jihuynh molssi025 silai zhlee
| |
| − | dabelinsky jihyepark molssi026 singanne zhonliang
| |
| − | dagolden jiikim molssi027 singh4 zhouyu1
| |
| − | dagrange jijin molssi028 sinhong zhuhli
| |
| − | daiwang jilao molssi029 sinlin zhuxie
| |
| − | dalpancakmak jiliu1 molssi030 sinsmith zhwong
| |
| − | damcintyre jimlin molssi031 sirle zhxia
| |
| − | damiruddin jimun molssi032 sishizawa zidiao
| |
| − | damoses jin molssi033 siskhakov ziguan
| |
| − | dandrew jinghzhou molssi034 siuchan zijiao
| |
| − | dangelidis jingwenli molssi035 siwewang zijizhou
| |
| − | danieliang jingwezhang molssi036 sixliu zikhan
| |
| − | danitorresra jingwliu molssi037 siyadav zilinchen
| |
| − | danizheng jinkokim molssi038 siyao zilwu
| |
| − | dantorres jinwang2 molssi039 siyimaya zirliu
| |
| − | dantyu jinwei morahimi siyzou zishao
| |
| − | danwei jinyhu moriasaranib sizahid ziweiwang
| |
| − | daoconnell jinyinwang mozhao sizzheng ziwyu
| |
| − | dappark jinyli mperess sjaffary zixli
| |
| − | darkow jinyuyang mpersch sjamshad ziyli
| |
| − | darlin jinyxu mpetrusky sjeevan ziyozhang
| |
| − | darvind jinzwang mpkatz sjens ziyye
| |
| − | darzeng jiqian mpsantomauro sjiecheng zkrayem
| |
| − | dathanasakos jiychong mquispecarba sjnelson zlyu
| |
| − | daultmccoy jiyim mradfar sjyang zmou
| |
| − | davidlin jiyjung mrahimibolda skade zniu
| |
| − | davizhao jiyounpark mrakhar skagana zoanderson
| |
| − | davliang jiyuliu mrashid skalam zoxie
| |
| − | davsilverman jiyuyang mrathore skalva zqiao
| |
| − | dawan jjcarter mrayeesuddin skann zsongzhu
| |
| − | dawei jjguo mrehan skapse zuzheng
| |
| − | dawendt jjjones mreuter skapur zwray
| |
| − | dawhu jjnielsen mrichter skarnik zye
| |
| − | daxxie jkable mrius skatariya zzaidi
| |
| − | dayeung jkiryluk mrkumar skavuri zzhuang
| |
| − | dayyan jkodner mrosati sketchum zzoya
| |
| − | dayyoon jkohara mrsun skobayashi
| |
| − | dbasu jkonopka msardis skogilathota
| |
| − | (base) [ehspector@milan1 home]$ cd ..
| |
| − | (base) [ehspector@milan1 gpfs]$ cd projects/AMS536
| |
| − | (base) [ehspector@milan1 AMS536]$ ls
| |
| − | 2017 2019 2021 2023 2025 junk.txt zzz.programs
| |
| − | 2018 2020 2022 2024 get_anchors.py zzz.anchors
| |
| − | (base) [ehspector@milan1 AMS536]$ cd zzz.programs/
| |
| − | (base) [ehspector@milan1 zzz.programs]$ ls
| |
| − | amber16 dock6.11 dock6-master.zip plot_footprint_single_magnitude.py
| |
| − | de_novo_anchors dock6.11_alpha dock_directory_arch plot_rmsds_amber
| |
| − | dock6.10 dock6.12 gen-frags-12 VS_libraries
| |
| − | dock6.10_milan dock6.12_ams536 old
| |
| − | (base) [ehspector@milan1 zzz.programs]$ cd dock6.12_ams536/
| |
| − | (base) [ehspector@milan1 dock6.12_ams536]$ ls
| |
| − | bin docs parameters README.md template_pipeline
| |
| − | developer install README src tutorials
| |
| − | (base) [ehspector@milan1 dock6.12_ams536]$ cd parameters/
| |
| − | (base) [ehspector@milan1 parameters]$ ls
| |
| − | 1 fraglib_linker.mol2 prot.table.ambcrg.sybH
| |
| − | antechamber fraglib_scaffold.mol2 sa_fraglib.dat
| |
| − | chem.defn fraglib_sidechain.mol2 screen.in
| |
| − | chemgrid fraglib_torenv.dat screen.para
| |
| − | chem_match.tbl leap vdw_AMBER_parm94.defn
| |
| − | flex.defn na.table.ambcrg vdw_AMBER_parm94.dock3_7.defn
| |
| − | flex_drive_mod.tbl pains_table_2019_09_01.dat vdw_AMBER_parm94.dock3_7_one_C_3.defn
| |
| − | flex_drive.tbl pains_table.dat vdw_AMBER_parm96.defn
| |
| − | flex_just_OH.defn ph4.defn vdw_AMBER_parm99.defn
| |
| − | flex_mod2.defn prot.table.ambcrg.ambH vdw_de_novo.defn
| |
| − | flex_mod.defn prot.table.ambcrg.pdb3H vdw.parms.amb
| |
| − | fraglib_ga_scaffold.mol2 prot.table.ambcrg.pdbH vdw.parms.update.amb
| |
| − | (base) [ehspector@milan1 parameters]$ pwd
| |
| − | /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters
| |
| − | (base) [ehspector@milan1 parameters]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/004_energymin/
| |
| − | (base) [ehspector@milan1 004_energymin]$ vi min.in
| |
| − | (base) [ehspector@milan1 004_energymin]$ touch max.in
| |
| − | (base) [ehspector@milan1 004_energymin]$ cd /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/
| |
| − | (base) [ehspector@milan1 dock6.12_ams536]$ ls
| |
| − | bin docs parameters README.md template_pipeline
| |
| − | developer install README src tutorials
| |
| − | (base) [ehspector@milan1 dock6.12_ams536]$ cd bin/
| |
| − | (base) [ehspector@milan1 bin]$ ls
| |
| − | am1bcc dock6.mpi multigrid_fp_gen.py sevsolv
| |
| − | amberize_complex espgen nchemgrid_GB showbox
| |
| − | amberize_ligand grid nchemgrid_SA showsphere
| |
| − | amberize_receptor grid-convert parmcal solvgrid
| |
| − | antechamber grid-convrds parmchk solvmap
| |
| − | atomtype make_phimap prepare_amber.pl sphere_selector
| |
| − | bondtype mol2bild.py prepare_rna_amber.pl sphgen
| |
| − | chemgrid mol2.py prepgen teLeap
| |
| − | combine_torenv.py mopac resp tleap
| |
| − | dock6 mopac.sh respgen
| |
| − | (base) [ehspector@milan1 bin]$ pwd
| |
| − | /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
| |
| − | (base) [ehspector@milan1 bin]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 004_energymin/
| |
| − | (base) [ehspector@milan1 004_energymin]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i max.in
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy [yes] (yes no):
| |
| − | internal_energy_rep_exp [12] ():
| |
| − | internal_energy_cutoff [100.0] ():
| |
| − | Note: Internal energy only includes repulsive VDW for growth and/or minimization.
| |
| − |
| |
| − | Molecule Library Input Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_atom_file [database.mol2] ():../001.structure/2ITO_ligand_Gefitinib_final.mol2
| |
| − | limit_max_ligands [no] (yes no):
| |
| − | skip_molecule [no] (yes no):
| |
| − | read_mol_solvation [no] (yes no):
| |
| − | calculate_rmsd [no] (yes no):yes
| |
| − | use_rmsd_reference_mol [no] (yes no):yes
| |
| − | rmsd_reference_filename [ligand_rmsd.mol2] ():../001.structure/2ITO_ligand_Gefitinib_final.mol2
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter [no] (yes no):
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand [yes] (yes no):no
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter [no] (yes no):
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules [yes] (yes no):
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary [no] (yes no):
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary [yes] (yes no):
| |
| − | grid_score_rep_rad_scale [1] ():
| |
| − | grid_score_vdw_scale [1] ():
| |
| − | grid_score_es_scale [1] ():
| |
| − | grid_lig_efficiency [no] (yes no):
| |
| − | grid_score_grid_prefix [grid] ():../003_gridbox/grid
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand [yes] (yes no):
| |
| − | simplex_max_iterations [1000] ():
| |
| − | simplex_tors_premin_iterations [0] ():
| |
| − | simplex_max_cycles [1] ():
| |
| − | simplex_score_converge [0.1] ():
| |
| − | simplex_cycle_converge [1.0] ():
| |
| − | simplex_trans_step [1.0] ():
| |
| − | simplex_rot_step [0.1] ():
| |
| − | simplex_tors_step [10.0] ():
| |
| − | simplex_final_min [no] (yes no):
| |
| − | simplex_random_seed [0] ():
| |
| − | simplex_restraint_min [no] (yes no):yes
| |
| − | simplex_coefficient_restraint [10.0] ():
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model [all] (all | united):
| |
| − | vdw_defn_file [vdw.defn] ():
| |
| − | flex_defn_file [flex.defn] ():
| |
| − | flex_drive_file [flex_drive.tbl] ():
| |
| − |
| |
| − | Molecule Library Output Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_outfile_prefix [output] ():
| |
| − | write_mol_solvation [no] (yes no):
| |
| − | write_orientations [no] (yes no):
| |
| − | num_scored_conformers [1] ():
| |
| − | score_threshold [100.0] ():
| |
| − | rank_ligands [no] (yes no):
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − |
| |
| − | Could not open vdw.defn for reading. Program will terminate.
| |
| − |
| |
| − | (base) [ehspector@milan1 004_energymin]$ vimdiff min.in max.in
| |
| − | 2 files to edit
| |
| − | (base) [ehspector@milan1 004_energymin]$ rm max.in
| |
| − | (base) [ehspector@milan1 004_energymin]$ vi min.sh
| |
| − | (base) [ehspector@milan1 004_energymin]$ vi min.in
| |
| − | (base) [ehspector@milan1 004_energymin]$ bash min.sh
| |
| − | (base) [ehspector@milan1 004_energymin]$ ls
| |
| − | 5een.lig.min_scored.mol2 min.in min.out min.sh
| |
| − | (base) [ehspector@milan1 004_energymin]$ vi min.out
| |
| − | (base) [ehspector@milan1 004_energymin]$ ls
| |
| − | 5een.lig.min_scored.mol2 min.in min.out min.sh
| |
| − | (base) [ehspector@milan1 004_energymin]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1086 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1086 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ mv 1086/ 1O86
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
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| − | (base) [ehspector@milan2 Tutorials]$ cp 2w26/commands.txt 1O86/commands.txt
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| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/
| |
| − | (base) [ehspector@milan2 1O86]$ ls
| |
| − | commands.txt
| |
| − | (base) [ehspector@milan2 1O86]$ bash commands.txt
| |
| − | (base) [ehspector@milan2 1O86]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore
| |
| − | [Bookmarked Feb 7, 2025 at 3:22:42 PM]
| |
| − | (base) [ehspector@milan2 1O86]$ mv 004_dock/ 004_energymin
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| − | (base) [ehspector@milan2 1O86]$ cd 001_structure/
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | 1O86_ligand_H_cH.mol2 1O86_protein_H_cH.mol2
| |
| − | 1O86_ligand_noH_nocH.mol2 1O86_protein_noH_nocH.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
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| − | 1O86_surface.dms
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 5EEN/
| |
| − | (base) [ehspector@milan2 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan2 5EEN]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 5een.sph 5een_surface.dms INSPH OUTSPH selected_spheres.sph select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
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| − | (base) [ehspector@milan2 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/sphere.sph 1O86/002_surface_spheres/sphere.sph
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| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/select.sph 1O86/002_surface_spheres/select.sph
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| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/INSPH 1O86/002_surface_spheres/INSPH
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| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/
| |
| − | (base) [ehspector@milan2 1O86]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 1O86_surface.dms INSPH select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
| |
| − | At line 131 of file sphgen.f (unit = 4)
| |
| − | Fortran runtime error: Cannot open file '5een_surface.dms': No such file or directory
| |
| − |
| |
| − | Error termination. Backtrace:
| |
| − | #0 0x7ffff7d54ca5 in already_open
| |
| − | at ../../../libgfortran/io/open.c:742
| |
| − | #1 0x404f73 in ???
| |
| − | #2 0x40117c in ???
| |
| − | #3 0x7ffff742958f in ???
| |
| − | #4 0x7ffff742963f in ???
| |
| − | #5 0x4011b4 in ???
| |
| − | #6 0xffffffffffffffff in ???
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
| |
| − | At line 125 of file sphgen.f (unit = 6)
| |
| − | Fortran runtime error: Cannot open file 'OUTSPH': File exists
| |
| − |
| |
| − | Error termination. Backtrace:
| |
| − | #0 0x7ffff7d54ca5 in already_open
| |
| − | at ../../../libgfortran/io/open.c:742
| |
| − | #1 0x404e9e in ???
| |
| − | #2 0x40117c in ???
| |
| − | #3 0x7ffff742958f in ???
| |
| − | #4 0x7ffff742963f in ???
| |
| − | #5 0x4011b4 in ???
| |
| − | #6 0xffffffffffffffff in ???
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
| |
| − | At line 125 of file sphgen.f (unit = 6)
| |
| − | Fortran runtime error: Cannot open file 'OUTSPH': File exists
| |
| − |
| |
| − | Error termination. Backtrace:
| |
| − | #0 0x7ffff7d54ca5 in already_open
| |
| − | at ../../../libgfortran/io/open.c:742
| |
| − | #1 0x404e9e in ???
| |
| − | #2 0x40117c in ???
| |
| − | #3 0x7ffff742958f in ???
| |
| − | #4 0x7ffff742963f in ???
| |
| − | #5 0x4011b4 in ???
| |
| − | #6 0xffffffffffffffff in ???
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 1086_new_surface.dms 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
| |
| − | At line 125 of file sphgen.f (unit = 6)
| |
| − | Fortran runtime error: Cannot open file 'OUTSPH': File exists
| |
| − |
| |
| − | Error termination. Backtrace:
| |
| − | #0 0x7ffff7d54ca5 in already_open
| |
| − | at ../../../libgfortran/io/open.c:742
| |
| − | #1 0x404e9e in ???
| |
| − | #2 0x40117c in ???
| |
| − | #3 0x7ffff742958f in ???
| |
| − | #4 0x7ffff742963f in ???
| |
| − | #5 0x4011b4 in ???
| |
| − | #6 0xffffffffffffffff in ???
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 1086_new_surface.dms 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi 1086_new_surface.dms
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi sphere
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 1086_new_surface.dms 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 1086_new_surface.dms 1O86_surface.dms INSPH select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 1086_new_surface.dms 1O86.sph 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 1086_new_surface.dms 1O86.sph 1O86_surface.dms INSPH OUTSPH select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan2 1O86]$ cd 001_structure/
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | 1O86_ligand_H_cH.mol2 1O86_protein_H_cH.mol2
| |
| − | 1O86_ligand_noH_nocH.mol2 1O86_protein_noH_nocH.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | 1O86_ligand_H_cH.mol2 1O86_protein_H_cH.mol2
| |
| − | 1O86_ligand_noH_nocH.mol2 1O86_protein_noH_nocH.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ bash select.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 1086_new_surface.dms 1O86_surface.dms OUTSPH select.sph
| |
| − | 1O86.sph INSPH selected_spheres.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi OUTSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 1086_new_surface.dms 1O86_surface.dms OUTSPH select.sph
| |
| − | 1O86.sph INSPH selected_spheres.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/showbox.sh 1O86/003_gridbox/showbox.sh
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/showbox.in 1O86/003_gridbox/showbox.in
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi showbox.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ bash showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 1O86.box.pdb showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/grid.sh 1O86/003_gridbox/grid.sh
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/003_gridbox/grid.in 1O86/003_gridbox/grid.in
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 1O86.box.pdb grid.in grid.sh showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ cd 001_structure/
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | 1O86_ligand_H_cH.mol2 1O86_protein_H_cH.mol2
| |
| − | 1O86_ligand_noH_nocH.mol2 1O86_protein_noH_nocH.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ bash grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 1O86.box.pdb grid.in grid.out grid.sh showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.out
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ bash grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 1O86.box.pdb grid.in grid.out showbox.in showbox.sh
| |
| − | grid.bmp grid.nrg grid.sh '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.sh 1O86/004_energymin/min.sh
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.in 1O86/004_energymin/min.in
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/004_energymin/
| |
| − | (base) [ehspector@milan2 004_energymin]$ vi min.in
| |
| − | (base) [ehspector@milan2 004_energymin]$ cd ../001_structure/
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | 1O86_ligand_H_cH.mol2 1O86_protein_H_cH.mol2
| |
| − | 1O86_ligand_noH_nocH.mol2 1O86_protein_noH_nocH.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ cd ../004_energymin/
| |
| − | (base) [ehspector@milan2 004_energymin]$ ls
| |
| − | min.in min.sh
| |
| − | (base) [ehspector@milan2 004_energymin]$ bash min.sh
| |
| − | (base) [ehspector@milan2 004_energymin]$ ls
| |
| − | 1O86.lig.min_scored.mol2 min.in min.out min.sh
| |
| − | (base) [ehspector@milan2 004_energymin]$ vi min.out
| |
| − | (base) [ehspector@milan2 004_energymin]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 2w26]$ cd 001_structure/
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | (base) [ehspector@milan2 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26_surface.dms INSPH sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
| |
| − | At line 328 of file sphgen.f
| |
| − | Fortran runtime error: Bad value during floating point read
| |
| − |
| |
| − | Error termination. Backtrace:
| |
| − | #0 0x7ffff7d59e39 in formatted_transfer_scalar_read
| |
| − | at ../../../libgfortran/io/transfer.c:1790
| |
| − | #1 0x7ffff7d5b535 in formatted_transfer
| |
| − | at ../../../libgfortran/io/transfer.c:2491
| |
| − | #2 0x4049e0 in ???
| |
| − | #3 0x40516a in ???
| |
| − | #4 0x40117c in ???
| |
| − | #5 0x7ffff742958f in ???
| |
| − | #6 0x7ffff742963f in ???
| |
| − | #7 0x4011b4 in ???
| |
| − | #8 0xffffffffffffffff in ???
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ rm 2w26_surface.dms
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26_surface.dms INSPH OUTSPH sphere.sph temp1.ms temp3.atc
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ rm temp1.ms
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ rm temp3.atc
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ rm OUTSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26_surface.dms INSPH sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi INSPH
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ bash sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26.sph 2w26_surface.dms INSPH OUTSPH sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/002_surface_spheres/select.sph 2w26/002_surface_spheres/select.sph
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26.sph 2w26_surface.dms INSPH OUTSPH select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ../001_structure/
| |
| − | (base) [ehspector@milan2 001_structure]$ ls
| |
| − | 2w26_ligand_H_cH.mol2 2w26_protein_H_cH.mol2
| |
| − | 2w26_ligand_noH_nocH.mol2 2w26_protein_noH_nocH.mol2
| |
| − | (base) [ehspector@milan2 001_structure]$ cd ../002_surface_spheres/
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ vi select.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ bash select.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ ls
| |
| − | 2w26.sph 2w26_surface.dms INSPH OUTSPH selected_spheres.sph select.sph sphere.sph
| |
| − | (base) [ehspector@milan2 002_surface_spheres]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd 003_gridbox/
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | grid.in grid.sh showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ rm '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | grid.in grid.sh showbox.in showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi showbox.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi showbox.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ bash showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 2w26.box.pdb grid.in grid.sh showbox.in '&showbox.log&' showbox.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.in
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ bash grid.sh
| |
| − | (base) [ehspector@milan2 003_gridbox]$ ls
| |
| − | 2w26.box.pdb grid.in grid.out showbox.in showbox.sh
| |
| − | grid.bmp grid.nrg grid.sh '&showbox.log&'
| |
| − | (base) [ehspector@milan2 003_gridbox]$ vi grid.out
| |
| − | (base) [ehspector@milan2 003_gridbox]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_dock 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 2w26]$ vi commands.txt
| |
| − | (base) [ehspector@milan2 2w26]$ mv 004_dock/ 004_energymin
| |
| − | (base) [ehspector@milan2 2w26]$ cd 004_energymin/
| |
| − | (base) [ehspector@milan2 004_energymin]$ ls
| |
| − | (base) [ehspector@milan2 004_energymin]$ ls
| |
| − | (base) [ehspector@milan2 004_energymin]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.in 2w26/004_energymin/min.in
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/004_energymin/
| |
| − | (base) [ehspector@milan2 004_energymin]$ vi min.in
| |
| − | (base) [ehspector@milan2 004_energymin]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/004_energymin/min.sh 2w26/004_energymin/min.sh
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan2 2w26]$ cd 004_energymin/
| |
| − | (base) [ehspector@milan2 004_energymin]$ vi min.sh
| |
| − | (base) [ehspector@milan2 004_energymin]$ bash min.sh
| |
| − | (base) [ehspector@milan2 004_energymin]$ ls
| |
| − | 2w26.lig.min_scored.mol2 min.in min.out min.sh
| |
| − | (base) [ehspector@milan2 004_energymin]$ vi min.out
| |
| − | (base) [ehspector@milan2 004_energymin]$ client_loop: send disconnect: Broken pipe
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/5EEN/002_surface_spheres/
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 5een.sph 5een_surface.dms INSPH OUTSPH selected_spheres.sph select.sph sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ vi select.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ home
| |
| − | (base) [ehspector@milan1 espector]$ cd 4s0v/
| |
| − | (base) [ehspector@milan1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@milan1 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@milan1 gas_teiger]$ ls
| |
| − | gas_2.in gas_3.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2
| |
| − | gas_2.out gas.in no_charge no_gas.out_scored.mol2
| |
| − | gas_3.in gas.out no_gas.in test.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ ls
| |
| − | gas_2.in gas_3.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2
| |
| − | gas_2.out gas.in no_charge no_gas.out_scored.mol2
| |
| − | gas_3.in gas.out no_gas.in test.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_2.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_2.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi test_mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi test.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas.out_scored.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ cd ../../builds/alpha_branch/src/dock
| |
| − | (base) [ehspector@milan1 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@milan1 dock]$ home
| |
| − | (base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/
| |
| − | (base) [ehspector@milan1 gas_teiger]$ pwd
| |
| − | /gpfs/projects/rizzo/espector/4s0v/gas_teiger
| |
| − | (base) [ehspector@milan1 gas_teiger]$ cp gas_2.in gas_4.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_2.out gas_4.in gas.out_scored.mol2 no_gas.out test_nocharge.mol2
| |
| − | 1AAQ_yesG.mol2 gas_3.in gas.in no_charge no_gas.out_scored.mol2
| |
| − | gas_2.in gas_3.out gas.out no_gas.in test.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_4.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_4.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_4.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 5EEN/
| |
| − | (base) [ehspector@milan1 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 002_surface_spheres/
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ ls
| |
| − | 5een.sph 5een_surface.dms INSPH OUTSPH selected_spheres.sph select.sph sphere.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ vi select.sph
| |
| − | (base) [ehspector@milan1 002_surface_spheres]$ home
| |
| − | (base) [ehspector@milan1 espector]$ cd ..
| |
| − | (base) [ehspector@milan1 rizzo]$ home
| |
| − | (base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/
| |
| − | (base) [ehspector@milan1 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_2.out gas_4.in gas.out no_gas.in test.mol2
| |
| − | 1AAQ_yesG.mol2 gas_3.in gas_4.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2
| |
| − | gas_2.in gas_3.out gas.in no_charge no_gas.out_scored.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ rm gas_4.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_4.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_2.out gas_4.in gas.out no_gas.in test.mol2
| |
| − | 1AAQ_yesG.mol2 gas_3.in gas_4.out gas.out_scored.mol2 no_gas.out test_nocharge.mol2
| |
| − | gas_2.in gas_3.out gas.in no_charge no_gas.out_scored.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_4.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_4.in -o gas_4.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_2.out gas_4.in gas.in no_charge no_gas.out_scored.mol2
| |
| − | 1AAQ_yesG.mol2 gas_3.in gas_4.out gas.out no_gas.in test.mol2
| |
| − | gas_2.in gas_3.out gas_4.out_scored.mol2 gas.out_scored.mol2 no_gas.out test_nocharge.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_4.out_scored.mol2
| |
| − | (base) [ehspector@milan1 gas_teiger]$ cp gas_4.in gas_5.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_5.in
| |
| − | (base) [ehspector@milan1 gas_teiger]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i gas_5.in -o gas_5.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ vi gas_5.out
| |
| − | (base) [ehspector@milan1 gas_teiger]$ home
| |
| − | (base) [ehspector@milan1 espector]$ cd builds/alpha_branch/src/dock
| |
| − | (base) [ehspector@milan1 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi rdtyper.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@milan1 dock]$ cd ..
| |
| − | (base) [ehspector@milan1 src]$ ls
| |
| − | accessories dock gbsa_grids Makefile rdkit tleap
| |
| − | antechamber docktools grid mopac6 resp
| |
| − | (base) [ehspector@milan1 src]$ cd dock
| |
| − | (base) [ehspector@milan1 dock]$ ls
| |
| − | amber_typer.cpp filter.o mem_info.h score_internal.cpp
| |
| − | amber_typer.h fingerprint.cpp mem_info.o score_internal.h
| |
| − | amber_typer.o fingerprint.h nab score_internal.o
| |
| − | base_grid.cpp fingerprint.o nabcode.h score_multigrid.cpp
| |
| − | base_grid.h fraggraph.cpp nab.h score_multigrid.h
| |
| − | base_grid.o fraggraph.h orient.cpp score_multigrid.o
| |
| − | base_mpi.cpp fraggraph.o orient.h score.o
| |
| − | base_mpi.h fragment.cpp orient.o score_ph4.cpp
| |
| − | base_mpi.o fragment.h rddrive.cpp score_ph4.h
| |
| − | base_score.cpp fragment.o rddrive.h score_ph4.o
| |
| − | base_score.h gasteiger.cpp rddrive.o score_sasa.cpp
| |
| − | base_score.o gasteiger.h rdtyper.cpp score_sasa.h
| |
| − | conf_gen_ag.cpp gasteiger.o rdtyper.h score_sasa.o
| |
| − | conf_gen_ag.h grid.cpp rdtyper.o score_solvent.cpp
| |
| − | conf_gen_ag.o grid.h README score_solvent.h
| |
| − | conf_gen_cg.cpp grid.o sasa.cpp score_solvent.o
| |
| − | conf_gen_cg.h gzstream sasa.h score_volume.cpp
| |
| − | conf_gen_cg.o hungarian.cpp sasa.o score_volume.h
| |
| − | conf_gen_dn.cpp hungarian.h score_amber.cpp score_volume.o
| |
| − | conf_gen_dn_ga.cpp hungarian.o score_amber.h simplex.cpp
| |
| − | conf_gen_dn_ga.h iso_align.cpp score_amber.o simplex.h
| |
| − | conf_gen_dn_ga.o iso_align.h score_chemgrid.cpp simplex.o
| |
| − | conf_gen_dn.h iso_align.o score_chemgrid.h sphere.cpp
| |
| − | conf_gen_dn.o library_file.cpp score_chemgrid.o sphere.h
| |
| − | conf_gen_ga.cpp library_file.h score.cpp sphere.o
| |
| − | conf_gen_ga.h library_file.o score_descriptor.cpp tnt
| |
| − | conf_gen_ga.o limit_max_change.cpp score_descriptor.h trace.cpp
| |
| − | conf_gen_hdb.cpp limit_max_change.h score_descriptor.o trace.h
| |
| − | conf_gen_hdb.h limit_max_change.o score_footprint.cpp trace.inl
| |
| − | conf_gen_hdb.o lol score_footprint.h trace.o
| |
| − | defreal.h Makefile score_footprint.o utils.cpp
| |
| − | dock.cpp master_conf.cpp score_gist.cpp utils.h
| |
| − | dockmol.cpp master_conf.h score_gist.h utils.o
| |
| − | dockmol.h master_conf.o score_gist.o version.h
| |
| − | dockmol.o master_score.cpp score.h xlogp.cpp
| |
| − | dock.o master_score.h score_hbond.cpp xlogp.h
| |
| − | filter.cpp master_score.o score_hbond.h
| |
| − | filter.h mem_info.cpp score_hbond.o
| |
| − | (base) [ehspector@milan1 dock]$ cd ..
| |
| − | (base) [ehspector@milan1 src]$ ls
| |
| − | accessories dock gbsa_grids Makefile rdkit tleap
| |
| − | antechamber docktools grid mopac6 resp
| |
| − | (base) [ehspector@milan1 src]$ cd ..
| |
| − | (base) [ehspector@milan1 alpha_branch]$ ks
| |
| − | -bash: ks: command not found
| |
| − | (base) [ehspector@milan1 alpha_branch]$ ls
| |
| − | bin docs parameters README.md template_pipeline
| |
| − | developer install README src tutorials
| |
| − | (base) [ehspector@milan1 alpha_branch]$ cd src/
| |
| − | (base) [ehspector@milan1 src]$ ls
| |
| − | accessories dock gbsa_grids Makefile rdkit tleap
| |
| − | antechamber docktools grid mopac6 resp
| |
| − | (base) [ehspector@milan1 src]$ cd ..
| |
| − | (base) [ehspector@milan1 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@milan1 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
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| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
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| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@milan1 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Mon Feb 10 01:24:01 PM EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from filter.h:10,
| |
| − | from filter.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from filter.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fingerprint.h:13,
| |
| − | from fingerprint.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from fingerprint.h:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fraggraph.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fraggraph.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fragment.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fragment.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from gasteiger.h:8,
| |
| − | from gasteiger.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from gasteiger.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from hungarian.h:7,
| |
| − | from hungarian.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from hungarian.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from library_file.h:9,
| |
| − | from library_file.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from library_file.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o limit_max_change.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from limit_max_change.h:12,
| |
| − | from limit_max_change.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from limit_max_change.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o master_conf.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from master_conf.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from master_conf.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o master_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from master_score.h:5,
| |
| − | from master_score.cpp:2:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from master_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | ^Cmake[1]: *** [../../install/rules.h:36: master_score.o] Interrupt
| |
| − | make: *** [Makefile:28: dock] Interrupt
| |
| − |
| |
| − | (base) [ehspector@milan1 install]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Permission denied, please try again.
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | (base) [ehspector@login2 ~]$ home
| |
| − | (base) [ehspector@login2 espector]$ cd builds/alpha_branch/install/
| |
| − | (base) [ehspector@login2 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@login2 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Mon Feb 10 13:29:04 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/haswell/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | ^Cmake[1]: *** [conf_gen_ag.o] Interrupt
| |
| − | make: *** [dock] Interrupt
| |
| − |
| |
| − | (base) [ehspector@login2 install]$ rdkit
| |
| − | bash: rdkit: command not found...
| |
| − | (base) [ehspector@login2 install]$ rd
| |
| − | srun: error: invalid partition specified: short-40core
| |
| − | srun: error: Unable to allocate resources: Invalid partition name specified
| |
| − | (base) [ehspector@login2 install]$ cd ..
| |
| − | (base) [ehspector@login2 alpha_branch]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ rd
| |
| − | srun: job 925032 queued and waiting for resources
| |
| − | srun: job 925032 has been allocated resources
| |
| − | (base) [ehspector@dn018 ~]$ home
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| − | (base) [ehspector@dn018 espector]$ cd builds/alpha_branch/install/
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| − | (base) [ehspector@dn018 install]$ make clean
| |
| − | make -C ../src clean
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| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
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| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
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| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn018 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Mon Feb 10 13:31:12 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from filter.h:10,
| |
| − | from filter.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from filter.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fingerprint.h:13,
| |
| − | from fingerprint.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from fingerprint.h:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fraggraph.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fraggraph.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fragment.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fragment.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from gasteiger.h:8,
| |
| − | from gasteiger.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from gasteiger.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from hungarian.h:7,
| |
| − | from hungarian.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from hungarian.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from library_file.h:9,
| |
| − | from library_file.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from library_file.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o limit_max_change.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from limit_max_change.h:12,
| |
| − | from limit_max_change.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from limit_max_change.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o master_conf.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from master_conf.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from master_conf.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o master_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from master_score.h:5,
| |
| − | from master_score.cpp:2:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from master_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o orient.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from orient.h:7,
| |
| − | from orient.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from orient.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o sasa.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from sasa.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from sasa.h:14:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o score_amber.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_amber.cpp:66:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
| |
| − | from score_amber.cpp:55:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o score_chemgrid.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_chemgrid.cpp:39:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
| |
| − | from score_chemgrid.cpp:38:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o score_descriptor.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_descriptor.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_descriptor.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o score_footprint.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_footprint.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_footprint.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o score_ph4.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_ph4.h:7,
| |
| − | from score_ph4.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_ph4.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o score_volume.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_volume.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_volume.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o score_gist.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_gist.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_gist.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o score_hbond.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_hbond.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_hbond.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o score_internal.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_internal.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_internal.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o score_multigrid.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_multigrid.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_multigrid.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o score_sasa.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from score_sasa.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_sasa.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o score_solvent.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from score_solvent.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_solvent.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o simplex.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from master_score.h:5,
| |
| − | from simplex.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from simplex.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o sphere.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o trace.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o utils.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from utils.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from utils.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o iso_align.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fragment.h:12,
| |
| − | from iso_align.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from fragment.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o mem_info.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o rdtyper.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
| |
| − | from rdtyper.cpp:18:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from rdtyper.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o rddrive.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from rddrive.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from dockmol.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | cd nab && make all
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | gcc -c -O3 -D_ANSI_SOURCE molio.c
| |
| − | gcc -c -O2 -o prm.o prm.c
| |
| − | make is_LEX_available
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c
| |
| − | gcc -c -O2 -o traceback.o traceback.c
| |
| − | gcc -c -O2 -o select_atoms.o select_atoms.c
| |
| − | gcc -c -O2 -o memutil.o memutil.c
| |
| − | gcc -c -O2 -o reslib.o reslib.c
| |
| − | gcc -c -O2 -o jacobi.o jacobi.c
| |
| − | gcc -c -O2 -o molutil.o molutil.c
| |
| − | gcc -c -O2 -o chirvol.o chirvol.c
| |
| − | gcc -c -O2 -o regexp.o regexp.c
| |
| − | gcc -c -O2 -o binpos.o binpos.c
| |
| − | gcc -c -O2 -o time.o time.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE rand2.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE conjgrad.c
| |
| − | gcc -c -O2 -o database.o database.c
| |
| − | gcc -c -O2 -o tleap.o tleap.c
| |
| − | ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
| |
| − | ar: creating nab.a
| |
| − | a - molio.o
| |
| − | a - prm.o
| |
| − | a - sff.o
| |
| − | a - traceback.o
| |
| − | a - select_atoms.o
| |
| − | a - memutil.o
| |
| − | a - reslib.o
| |
| − | a - jacobi.o
| |
| − | a - molutil.o
| |
| − | a - chirvol.o
| |
| − | a - regexp.o
| |
| − | a - binpos.o
| |
| − | a - time.o
| |
| − | a - rand2.o
| |
| − | a - conjgrad.o
| |
| − | a - database.o
| |
| − | a - tleap.o
| |
| − | ranlib nab.a
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
| |
| − | ar cr libgzstream.a gzstream.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
| |
| − | -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
| |
| − | mv dock6.rdkit ../../bin
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − |
| |
| − | Installation of
| |
| − | DOCK v6.12
| |
| − | program dock is complete at Mon Feb 10 13:34:18 EST 2025.
| |
| − |
| |
| − | (base) [ehspector@dn018 install]$ exit
| |
| − | exit
| |
| − | (base) [ehspector@milan1 ~]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ home
| |
| − | (base) [ehspector@milan1 espector]$ cd ..
| |
| − | (base) [ehspector@milan1 rizzo]$ module load git
| |
| − | (base) [ehspector@milan1 rizzo]$ home
| |
| − | (base) [ehspector@milan1 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@milan1 espector]$ git status
| |
| − | fatal: not a git repository (or any parent up to mount point /)
| |
| − | Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
| |
| − | (base) [ehspector@milan1 espector]$ cd builds/
| |
| − | (base) [ehspector@milan1 builds]$ cd alpha_branch/
| |
| − | (base) [ehspector@milan1 alpha_branch]$ git status
| |
| − | On branch alpha_branch
| |
| − | Your branch is up to date with 'origin/alpha_branch'.
| |
| − |
| |
| − | Changes not staged for commit:
| |
| − | (use "git add <file>..." to update what will be committed)
| |
| − | (use "git restore <file>..." to discard changes in working directory)
| |
| − | modified: docs/new_in_6.13.txt
| |
| − | modified: src/dock/filter.cpp
| |
| − |
| |
| − | Untracked files:
| |
| − | (use "git add <file>..." to include in what will be committed)
| |
| − | src/dock/lol
| |
| − | src/rdkit/boost/
| |
| − | src/rdkit/boost_1_71_0.tar.gz
| |
| − | src/rdkit/boost_1_71_0/
| |
| − | src/rdkit/eigen-3.3.9.tar.gz
| |
| − | src/rdkit/eigen-3.3.9/
| |
| − | src/rdkit/rdkit-Release_2019_09_1.tar.gz
| |
| − | src/rdkit/rdkit-Release_2019_09_1/
| |
| − |
| |
| − | no changes added to commit (use "git add" and/or "git commit -a")
| |
| − | (base) [ehspector@milan1 alpha_branch]$ git commit src/dock/filter.cpp
| |
| − | Aborting commit due to empty commit message.
| |
| − | (base) [ehspector@milan1 alpha_branch]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan1 2w26]$ cd 005_virtual_screen/
| |
| − | (base) [ehspector@milan1 005_virtual_screen]$ ls
| |
| − | (base) [ehspector@milan1 005_virtual_screen]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ mv 005_virtual_screen/ 005_footprint/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_footprint 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan1 2w26]$ cd 005_footprint/
| |
| − | (base) [ehspector@milan1 005_footprint]$ ls
| |
| − | (base) [ehspector@milan1 005_footprint]$ touch footprint.in
| |
| − | (base) [ehspector@milan1 005_footprint]$ ls
| |
| − | footprint.in
| |
| − | (base) [ehspector@milan1 005_footprint]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cd 004_energymin/
| |
| − | (base) [ehspector@milan1 004_energymin]$ ls
| |
| − | 2w26.lig.min_scored.mol2 min.in min.out min.sh
| |
| − | (base) [ehspector@milan1 004_energymin]$ vi 2w26.lig.min_scored.mol2
| |
| − | (base) [ehspector@milan1 004_energymin]$ ls
| |
| − | 2w26.lig.min_scored.mol2 min.in min.out min.sh
| |
| − | (base) [ehspector@milan1 004_energymin]$ vi min.s
| |
| − | (base) [ehspector@milan1 004_energymin]$ vi min.sh
| |
| − | (base) [ehspector@milan1 004_energymin]$ cd ../
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_footprint 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan1 2w26]$ vi commands.txt
| |
| − | (base) [ehspector@milan1 2w26]$ cd ,,
| |
| − | -bash: cd: ,,: No such file or directory
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_footprint 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan1 2w26]$ cd 005_footprint/
| |
| − | (base) [ehspector@milan1 005_footprint]$ ls
| |
| − | footprint.in
| |
| − | (base) [ehspector@milan1 005_footprint]$ mv footprint.in rigid.in
| |
| − | (base) [ehspector@milan1 005_footprint]$ vi rigid.sh
| |
| − | (base) [ehspector@milan1 005_footprint]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ mv 005_footprint/ 005_rigid
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_rigid 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan1 2w26]$ cd 005_rigid/
| |
| − | (base) [ehspector@milan1 005_rigid]$ ls
| |
| − | rigid.in rigid.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ bash rigid.
| |
| − | bash: rigid.: No such file or directory
| |
| − | (base) [ehspector@milan1 005_rigid]$ bash rigid.sh
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy [yes] (yes no):
| |
| − | internal_energy_rep_exp [12] ():
| |
| − | internal_energy_cutoff [100.0] ():
| |
| − | Note: Internal energy only includes repulsive VDW for growth and/or minimization.
| |
| − |
| |
| − | Molecule Library Input Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_atom_file [database.mol2] ():
| |
| − | limit_max_ligands [no] (yes no):
| |
| − | skip_molecule [no] (yes no):
| |
| − | read_mol_solvation [no] (yes no):
| |
| − | calculate_rmsd [no] (yes no):
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter [no] (yes no):
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand [yes] (yes no):
| |
| − | automated_matching [yes] (yes no):
| |
| − | receptor_site_file [receptor.sph] ():
| |
| − | max_orientations [1000] ():
| |
| − | critical_points [no] (yes no):
| |
| − | chemical_matching [no] (yes no):
| |
| − | use_ligand_spheres [no] (yes no):
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter [no] (yes no):
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules [yes] (yes no):
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary [no] (yes no):
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary [yes] (yes no):
| |
| − | grid_score_rep_rad_scale [1] ():
| |
| − | grid_score_vdw_scale [1] ():
| |
| − | grid_score_es_scale [1] ():
| |
| − | grid_lig_efficiency [no] (yes no):
| |
| − | grid_score_grid_prefix [grid] ():
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand [yes] (yes no):
| |
| − | simplex_max_iterations [1000] ():
| |
| − | simplex_tors_premin_iterations [0] ():
| |
| − | simplex_max_cycles [1] ():
| |
| − | simplex_score_converge [0.1] ():
| |
| − | simplex_cycle_converge [1.0] ():
| |
| − | simplex_trans_step [1.0] ():
| |
| − | simplex_rot_step [0.1] ():
| |
| − | simplex_tors_step [10.0] ():
| |
| − | simplex_final_min [no] (yes no):
| |
| − | simplex_random_seed [0] ():
| |
| − | simplex_restraint_min [no] (yes no):
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model [all] (all | united):
| |
| − | vdw_defn_file [vdw.defn] ():
| |
| − | flex_defn_file [flex.defn] ():
| |
| − | flex_drive_file [flex_drive.tbl] ():
| |
| − |
| |
| − | Molecule Library Output Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_outfile_prefix [output] ():
| |
| − | write_mol_solvation [no] (yes no):
| |
| − | write_orientations [no] (yes no):
| |
| − | num_scored_conformers [1] ():
| |
| − | score_threshold [100.0] ():
| |
| − | rank_ligands [no] (yes no):
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − |
| |
| − | Could not open vdw.defn for reading. Program will terminate.
| |
| − |
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 005_rigid]$ rm rigid.in
| |
| − | (base) [ehspector@milan1 005_rigid]$ touch rigid.in
| |
| − | (base) [ehspector@milan1 005_rigid]$ ls
| |
| − | rigid.in rigid.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 005_rigid]$ bash rigid.sh
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy [yes] (yes no):
| |
| − | internal_energy_rep_exp [12] ():
| |
| − | internal_energy_cutoff [100.0] ():
| |
| − | Note: Internal energy only includes repulsive VDW for growth and/or minimization.
| |
| − |
| |
| − | Molecule Library Input Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_atom_file [database.mol2] ():2w26.lig.min.mol2
| |
| − | limit_max_ligands [no] (yes no):
| |
| − | skip_molecule [no] (yes no):
| |
| − | read_mol_solvation [no] (yes no):
| |
| − | calculate_rmsd [no] (yes no):yes
| |
| − | use_rmsd_reference_mol [no] (yes no):yes
| |
| − | rmsd_reference_filename [ligand_rmsd.mol2] ():2w26.lig.min.mol2
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter [no] (yes no):
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand [yes] (yes no):
| |
| − | automated_matching [yes] (yes no):
| |
| − | receptor_site_file [receptor.sph] ():../002_surface_spheres/selected_spheres.sph
| |
| − | max_orientations [1000] ():
| |
| − | critical_points [no] (yes no):
| |
| − | chemical_matching [no] (yes no):
| |
| − | use_ligand_spheres [no] (yes no):
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter [no] (yes no):
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules [yes] (yes no):
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary [no] (yes no):
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary [yes] (yes no):
| |
| − | grid_score_rep_rad_scale [1] ():
| |
| − | grid_score_vdw_scale [1] ():
| |
| − | grid_score_es_scale [1] ():
| |
| − | grid_lig_efficiency [no] (yes no):
| |
| − | grid_score_grid_prefix [grid] ():../003_gridbox/grid
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand [yes] (yes no):
| |
| − | simplex_max_iterations [1000] ():
| |
| − | simplex_tors_premin_iterations [0] ():
| |
| − | simplex_max_cycles [1] ():
| |
| − | simplex_score_converge [0.1] ():
| |
| − | simplex_cycle_converge [1.0] ():
| |
| − | simplex_trans_step [1.0] ():
| |
| − | simplex_rot_step [0.1] ():
| |
| − | simplex_tors_step [10.0] ():
| |
| − | simplex_final_min [no] (yes no):
| |
| − | simplex_random_seed [0] ():
| |
| − | simplex_restraint_min [no] (yes no):
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model [all] (all | united):
| |
| − | vdw_defn_file [vdw.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/vdw_AMBER_parm99.defn
| |
| − | flex_defn_file [flex.defn] ():
| |
| − | flex_drive_file [flex_drive.tbl] ():
| |
| − |
| |
| − | Molecule Library Output Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_outfile_prefix [output] ():rigid.out
| |
| − | write_mol_solvation [no] (yes no):
| |
| − | write_orientations [no] (yes no):
| |
| − | num_scored_conformers [1] ():
| |
| − | score_threshold [100.0] ():
| |
| − | rank_ligands [no] (yes no):
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − |
| |
| − | Could not open flex.defn for reading. Therefore we will use default parameters: /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
| |
| − |
| |
| − |
| |
| − |
| |
| − | Could not open flex_drive.tbl for reading. Therefore we will use default parameters: /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
| |
| − |
| |
| − | Initializing Library File Routines...
| |
| − |
| |
| − |
| |
| − |
| |
| − | Could not open 2w26.lig.min.mol2 for reading. Program will terminate.
| |
| − |
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 005_rigid]$ cp rigid.sh rigid_2.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid_2.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ ls
| |
| − | rigid_2.sh rigid.in rigid.out rigid.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.out
| |
| − | (base) [ehspector@milan1 005_rigid]$ cd ../004_energymin/
| |
| − | (base) [ehspector@milan1 004_energymin]$ ls
| |
| − | 2w26.lig.min_scored.mol2 min.in min.out min.sh
| |
| − | (base) [ehspector@milan1 004_energymin]$ cd ../005_rigid/
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ ls
| |
| − | rigid_2.sh rigid.in rigid.out rigid.out_scored.mol2 rigid.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.out
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ ls
| |
| − | rigid_2.sh rigid.in rigid.out rigid.out_scored.mol2 rigid.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.out
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2
| |
| − | (base) [ehspector@milan1 005_rigid]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ mv 006_virtual_screen_mpi/ 006_flex_docking
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_rigid 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_flex_docking 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan1 2w26]$ cd 005_rigid/
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid_2.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 005_rigid]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_rigid 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_flex_docking 008_rescore Notes.txt
| |
| − | (base) [ehspector@milan1 2w26]$ cd 001_structure
| |
| − | (base) [ehspector@milan1 001_structure]$ ls
| |
| − | 2w26_ligand_H_cH.mol2 2w26_protein_H_cH.mol2
| |
| − | 2w26_ligand_noH_nocH.mol2 2w26_protein_noH_nocH.mol2
| |
| − | (base) [ehspector@milan1 001_structure]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cd 005_rigid/
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ ls
| |
| − | rigid_2.sh rigid.in rigid.out rigid.out_scored.mol2 rigid.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.out_scored.mol2
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.out
| |
| − | (base) [ehspector@milan1 005_rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 005_rigid]$ bash rigid_2.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ ls
| |
| − | rigid_2.sh rigid.in rigid.out rigid.out_conformers.mol2 rigid.out_scored.mol2 rigid.sh
| |
| − | (base) [ehspector@milan1 005_rigid]$ grep -c "Name" rigid.out_scored.mol2
| |
| − | 7
| |
| − | (base) [ehspector@milan1 005_rigid]$ client_loop: send disconnect: Broken pipe
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ ls
| |
| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@milan1 ~]$ cd AMS_536/
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd ..
| |
| − | (base) [ehspector@milan1 ~]$ cd ..
| |
| − | (base) [ehspector@milan1 home]$ ls
| |
| − | caaachase dbobo jksullivan msazonova skorada
| |
| − | aaaggarwal dcalabria jktsui mschedel skotelnikov
| |
| − | aaaggarwal.26FEB2020 dcazorla jleehand mschrimpf skotla
| |
| − | aabdurrob dcbrown jlfong mschwaller skrichevsky
| |
| − | aabhilash dcharan jlguerra mshaaban skristam
| |
| − | aadarsh dchien jlipshultz mshahneousba skrupp
| |
| − | aadubois ddassanis jlomanto mshih sladerwager
| |
| − | aagashe ddelayo jluceno mshinder slakshminara
| |
| − | aagishtein ddemartini jlungu mshu slaverty
| |
| − | aahern ddukes jlutsky msilfies slthomas
| |
| − | aaiyer deachen jlweissman msmoawad smadishetty
| |
| − | aajith decarlson jmaghakian msrao smaiti
| |
| − | aakale dekblom jmarcantonio msreeves smallipattu
| |
| − | aakiti delam jmarciano mstanacevic smamalis
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| − | aakkumar demccabe jmayortorres msweber smartynenko
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| − | aaksenova dereliu jmeliker mtalukder smascarenhas
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| − | aaliang deroy jmendezmende mthu smconnors
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| − | aallin devlin jmgentile mtoledorozyc smdick
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| − | aallu dfarahmandpo jmiao mtsonev smedved
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| − | aalpern dfei jmitchell mturk smeghdadizan
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| − | aamahmood dfucich jmorkos mumarani smelhiraj
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| − | aambrown dgaidhani jmulackal muprit smesiha
| |
| − | aamgalan dgenet jmurrugarral mvalakonda smhenry
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| − | aaminev dgersappe jmurzaku mvashishtha smiduthuri
| |
| − | aamurthy dg-mgmt1-auth-keys jmvasquez mvfernandezs smilakovic
| |
| − | aanaggarwal dg-mgmt2-auth-keys jnassar mvilensky smirghafouri
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| − | aanagnostopo dgnatenko jnatarajan mwilking smirroshande
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| − | aanik dgoon jnery myarif smofakham
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| − | aaprasad dgruzdev jnicasio myearsley smui
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| − | aarasappan dgursoy jnmauro myoungblood smukherjee
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| − | aarefin dgwood jnong mysql smvaccaro
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| − | aarmas dhailegeorgi joawilson mzamani snarmeen
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| − | aarroyave dhamam jocai mzepedaaguil snigam
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| − | aasim dhandzlik jocwilliams mzhang snikhil
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| − | aaslov dhdesouza jodey naahassan snimatullo
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| − | aates dhildreth jodoh nabchowdhury snizambad
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| − | aaurora dhongyi jodweinstein nabsyed snolas
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| − | aavadhani dhperumal joeleung nacchen snyman
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| − | aavira dhualong joeychan nacharya soba
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| − | aaydin diannace jofranklin nagnihotri sochakrabort
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| − | aaysheth disandovalch johbernard nagutierrez sohshin
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| − | ababbar diwliu johnliu nalewis sohtsuka
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| − | abadhe djagnarain joifan nanqwang solhapark
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| − | abahadori djgold jomyoung napopova somishra
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| − | abaidya djlambert jonamartins naqiu somunoz
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| − | aball djoh jonicholson nasweet sooapark
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| − | abardizbania djulian jonsu natsai sopjang
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| − | abbhaskar djyu jonyin nazzhou sortizbetanc
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| − | abeahmad dkadams joolee nbalasubrama sosarangi
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| − | abenslama dkharzeev joosuh nbasok sosuresh
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| − | abialkowska dkirby joroiland nbayas sowu
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| − | abjoshi dkozakov joshmathew nbodduluri sozturk
| |
| − | abkanevsky dkunjadiya joshumartin nbosviel spaci
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| − | abogetti dlanger jovvazquezri nbowers spandrekar
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| − | aborad dlhe joying nciotoli spang
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| − | aborcatasciu dlucksted jozhao ncmeloottu spapazahario
| |
| − | aborger dmahalli jpantano ncpathak spapazis
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| − | aborowicz dmahzabin jparise ndcertain sparvathredd
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| − | abozin dmale jparkinson ndev spathrose
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| − | abphilip dmarkov jpascal ndheilly spilkey
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| − | abrady dmarr jpcastillo ndigrandi spiret
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| − | absalem dmckinnon jperezrios ndnguyen splee
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| − | abtambe dmirfenderes jpeshansky ndokania spochron
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| − | aburford dmorenosanti jpitt ndurand spothumahant
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| − | acage dmukherjee jpmoryl ndzikowski spriyadarsha
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| − | acalder dmulbagalven jporavanthat nesteves spugach
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| − | acali dnanjappa jpwhite nexposescan sqavi
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| − | acamino dnimatullo jqxiao neyang srahmani
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| − | acastiblanco dnterry jranjan nezheng sraisinghani
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| − | accapua dobyrne jrawski nfaiza sramanarajan
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| − | acchakravart dochoi jrcheung nfpugliese sramanarajan.OLD
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| − | acherath dofu jrcorbett nganu sramjan
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| − | achouhan dohhlee jrest nghoang sramstrom
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| − | acmarra dokkang jrgorman ngitman srashidian
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| − | adamare dongsong jrimel ngluck sretineni
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| − | adanial dongwhan jrkamler ngujarati srgupte
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| − | adanoji donshi jrleeman nhamdan srnalluri
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| − | adharan dotan jrojahn nhirtle srpayne
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| − | adiloreto doyjang jrutledge nichaturvedi srshende
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| − | ading dozhong jrwei nidimeglio ssabaghian
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| − | admannino dpadhorny jsaldivar nigreen ssagynbayeva
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| − | adpeng dpare jsalley nileong ssandal
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| − | adpollack dparedesmeri jsaltz niranmanesh ssarnot
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| − | adrana dparwana jsaputo nisankar ssarwar
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| − | adrflorio dpati jsaxena nisong sseepersaud
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| − | adrogers dpatil jscanderson nisoni ssemerkant
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| − | adubey dpenchoff jschuchart nivsingh sserbin
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| − | adutt dpfennell jschwedes njschwartzap sshaharia
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| − | aecuomo dpotemkin jseeliger nkahmed sshapourmian
| |
| − | aeichert drendina jseol nkandru ssheikhi
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| − | aeltareb drhamilton jsgordon nkatla sshoque
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| − | aeweiss dschneble jsinanan nkdean sshrestha
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| − | afahmed dseddoh jsistla nkeer sshrivastava
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| − | afarhadzadeh dsforza jskowalski nkhalsa ssivalenka
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| − | afgregory dshangase jslogan nkhandagale ssjohn
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| − | afrigo dsingla jsmaers nkhatri sskiena
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| − | afurey dsli jsmucker nkinalis ssomani
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| − | agaffoor dslo jsteier nkinlock ssperrottet
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| − | agaikwad dsmolarski jsuchan nkyose sstoller
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| − | agarforth dstepanenko jtalaveragre nleak sstoyanov
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| − | agargueta dstrenski jtekverk nlogozzo ssundar
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| − | agauer dswesty jtepan nlrogers ssunia
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| − | aghai dthanassi jtevans nmahamud ssyedfahad
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| − | agilgomez dtpham jtgabrielli nmaher ssyritsyn
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| − | agmaharaj dtsybychev jtjones nmanzella staralekar
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| − | agnsinha dtung jtmessina nmarcella stawong
| |
| − | agopalkrishn duwwang jtrelewicz nmathew stelehany
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| − | agraikos dvahabli jtrue nmehanna sthaker
| |
| − | agugel dvyas juaalcantara nmeister sthorgusen
| |
| − | agulhane dwhitty juffeng nmenasche stjjiang
| |
| − | ahalwah dwiczer julima nmendiratta stmandell
| |
| − | ahc dwillcox juliwu nmeruva stmccabe
| |
| − | ahmkhan dzavala jumma nmichielsen stomar
| |
| − | ahomayounnik dziadlou junding nmitra stpak
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| − | ahsingh eadas jungshwang nnadkarni strainer
| |
| − | ahurtado earavera junholee nnaitlho ststern
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| − | ahxiao eatkinson junhuzhang nnakka stuznik
| |
| − | aicheng ebagherizade junhyelee nnawal stzeng
| |
| − | aidnani ebartlett junjiang nnehaindrani stzou
| |
| − | ailyu eboria junkang nnghiemvu sudkhan
| |
| − | airussell ebreen junszhou nniemiec sukkumar
| |
| − | ajacovelli ebremer juntyao noibrahim sunarasimhas
| |
| − | ajalwan ebrini junwang5 nolconner sunarasimhas.OLD
| |
| − | ajamieson ebryski junxialiu novsingh sunghucho
| |
| − | ajasniew ecarcelespov junywang npahlavan sunkim2
| |
| − | ajchan ecgross jusandoval npanagodawet surmy
| |
| − | ajchavez echurch juschan nparghi sushahid
| |
| − | ajhong eclemmon jusliu npasari suwei
| |
| − | ajkoller ecline jusong npayen svadnerkar
| |
| − | ajlli ecoutsias justili npomata svaldez
| |
| − | ajmasella ecowley jusu npregosin svanderpoel
| |
| − | ajoung edeturk juychen nrajput svayasi
| |
| − | ajscarlatos edma juyyan nramdin svee
| |
| − | ajtran edowney juzou nreaton swaxman
| |
| − | ajwelsh edzhang jvansnellenb nsalekfarama swchaudhury
| |
| − | ajyadav eeryildiz jvaska nsampson swen
| |
| − | akalugade efinson jverbaarscho nsehgal sweverma
| |
| − | akanodia egebb jvishal nshouman swpaul
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| − | akapote egentles jvpepe nsimakov sxchen
| |
| − | akarkare egouvis jvu nsipperly syaddanapudi
| |
| − | akarzai eheywood jwahhab nsmehta syalla
| |
| − | akaufman ehspector jwcross nsoder syarma
| |
| − | akhibovska ejcarey jwcusick nsokolow syatigala
| |
| − | akhosronejad ejguan jwisdom nsomani syatskar
| |
| − | akhoukhi ejli jwlodek nstreb sydiaz
| |
| − | akingan ejohnfelt jxue ntadler syousef
| |
| − | akirillov ekandov jyerrick ntardugno sytlee
| |
| − | akkale ekbetancourt jyluo ntetrault tabhatia
| |
| − | akonosky ekeck jzoodsma ntippabhatla tadoyle
| |
| − | akravchuk ekeough kabichandani ntripti taeklee
| |
| − | akrowe ekhew kadeng nvafaeinajaf taeyounkim
| |
| − | aktyagi eklau kadiallo nvitek tagiles
| |
| − | akucich ekoo kadill nvohra tahkhan
| |
| − | akuduregundi elari kadreher nvsutherland tajjung
| |
| − | akundhuru elettieri kafarber nwein takther
| |
| − | akverma elgchan kaifzheng nwweber talama
| |
| − | akwakye elharris kaili nxlee talare
| |
| − | alabella eli kailiu2 nyfletcher talin
| |
| − | alaing ellai kailjiang obellinson tallison
| |
| − | alanhuang elleisenberg kaimxu odeshpande tamislam
| |
| − | alchung elmlowe kaitong odiamond tanis
| |
| − | aldong elogeswar kaixichen odickerson taryu
| |
| − | aldraper elslattery kamhassan oeskiocak tbabu
| |
| − | alehsu emacosta kamrivera ohaputhanthr tbertino
| |
| − | alem emarants kanagarwal ohyejin tbrackins
| |
| − | alexhernande emarkowitz kanzhao okim tbrinckmann
| |
| − | alfwu emarzigliano kapatel okoren tbrinkley
| |
| − | algrullon embriggs kaporter omcgranaghan tburfeind
| |
| − | alhhuang emrlin kapu omorozova tbushra
| |
| − | alianwar emroberts karamachandr omoy tcanli
| |
| − | alicwang emyhand kargill onatu tchatterton
| |
| − | alietzau enebet kasong oogunfolakan tchristy
| |
| − | alifeng eoruro katalwar ooreilly tchugh
| |
| − | aliguori eozkirimli katschmidt orambow tcotroneo
| |
| − | alindquist epapadopoulo kbaylous osdeshpande tdawar
| |
| − | allekim erandhawa kbdiaz oshakkour tdiprima
| |
| − | allelin eraut kbeckerredd oshetty tdviri
| |
| − | allwong erbraun kbelfon osteele tema
| |
| − | almabraham erfan kberard oyang testro
| |
| − | almishra erglukhov kberghaus oyasar tgavryshko
| |
| − | alokre ericlin1 kccoughlin padari tglotch
| |
| − | alowell erizhou kchetan paggarwal tgrgas
| |
| − | alperezmendo erkumar kchitale pahan tgrossberndt
| |
| − | alqin erluo kdas pallen tguttula
| |
| − | alsli erosenberg kdavidson pamishra thamada
| |
| − | alvhsu errjones kdehmelt parjain thausch
| |
| − | alynegron erschroeder kdemir parmitage thdavidson
| |
| − | amacinnis erwhuang kdevedzhiev patflanagan therault
| |
| − | amaffei esahin kdhar patmuller therodrigues
| |
| − | amanagarwal esalman kdhuri pavkirkar thollis
| |
| − | amanpsingh esaraivanov kdyro pavnkaur thomlin
| |
| − | amanzoor eschiltzrous kebui pawu thren
| |
| − | amaresca eshaji keckartt payao thzhou
| |
| − | amarya eshetreatkle kelam pb tianyuawang
| |
| − | amassari eshih keliao pbaliga tili
| |
| − | amasuno eshuryak kellywang pcascantebon timji
| |
| − | ambbrown esicoli kelvlin pcastillo timshi
| |
| − | amccumber esiegmann kenchin pchinthamred tinggao
| |
| − | amcelroy esogut kenhu pdalaya tinghwu
| |
| − | amchale esonmez kennwu pdamore tingliu2
| |
| − | amcpherran essingh kereid pdevarajan tingslin
| |
| − | amehla eswong kerwood pdjuric tinliu
| |
| − | amehmood etakeuchi kevazquez pdonat tiwwong
| |
| − | amgondal etalis kevcai pdongle tixi
| |
| − | amibrahim etchan kevcheng pdutta tiyuan
| |
| − | amigues etcheung keviliu pechang tjarrett
| |
| − | amisaha ethresher kevwei peihsieh tjohannessen
| |
| − | amkgupta etmonaco kexi peinwang tkarwal
| |
| − | amnoonan etrommer kfatema penzhang tknoll
| |
| − | amohamed etsang kfernando pesun tkohlmann
| |
| − | amohammadrez etwest kflora pferrero tkral
| |
| − | amohanty etyen kfryer pgaikar tkurc
| |
| − | amohideen evalin kgarg pganapathi tla
| |
| − | amoonilal evaxie kgayadhankar pganesh tlata
| |
| − | amrabet evergaracobo kgcassar pgodoy tloden
| |
| − | amramroop evxie kgjonas pgoldbart tlonsway
| |
| − | amrangwala ewpeterson kgoranta pgoriparthi tmcgee
| |
| − | amritpsingh exiu kgulati pgubbala tmia
| |
| − | amullhaupt eylei khajny pguo tmohandas
| |
| − | amychen5 eyzhu khasegawa pgurung tmoriya
| |
| − | amyla fabdinov khoh phariprasad tmsmyth
| |
| − | anadelgado faliang khumphries phowlader tmuntean
| |
| − | analekseenko falmodaresit khyunjae phtnguyen tnle
| |
| − | anarora faluo kihan phyeh tnsingletary
| |
| − | ancollins fang1 kim128 pinlee toneal
| |
| − | andcheung fanliu2 kim169 pinliu toye
| |
| − | andguo fannli kim65 pjgriffin tpalit
| |
| − | andgutierrez fanwang1 kingle pkaelbling tqduong
| |
| − | andrchu faoki kipoon pkayedpour tqle
| |
| − | andrwu faslanbeigi kisrani pkidambi traj
| |
| − | andylin2 fatrahman kissung pkottapalli trichen
| |
| − | anearora fatsai kjamal pkrstic trli
| |
| − | anegi faye kjayanettiar pkuan trosenlicht
| |
| − | aneiman fayyang kjroberts pkwoczak tsclement
| |
| − | anejoshi fbasharat kjtorres pliu tshrestha
| |
| − | anejoshi.OLD fbischoff kjun plorenagodoy tsinghal
| |
| − | anemajerova fcherat kkamate pmao tslewis
| |
| − | anfrenkel fcornejofern kkannapur pmarla tsmiley
| |
| − | angderosa fcoskun kkasarapu pmatera tteng
| |
| − | aniksingh feliang kkasavajhala pmcdowall tthakir
| |
| − | anisrinivasa fenzhang kkaushik pmdunge tthulasidas
| |
| − | anjmoore fewang kkayang pmeade ttnnguyen
| |
| − | ankmaheshwar feyeh kkirane pmeda ttom
| |
| − | ankrishnan fgao kkostyszyn pmmehta tweinacht
| |
| − | anltran fhchaudhry kkui pmscully tweiwei
| |
| − | annicoll fiburke kkurti pmuzac twymore
| |
| − | anpnguyen fiowong kkyeong pnalluri txiang
| |
| − | anpurwar fjalia klanzetta pnookala tye
| |
| − | ansabharwal fjangchup klhudson podonnell tyeh
| |
| − | ansgandhi fkarankumar kljjohnson ppolak tyokoyama
| |
| − | anshen fkhondker kllivichuzca ppriyadarshi tzwei
| |
| − | anslade fladeind kmadanahitib praagarwal uarora
| |
| − | anthochen fluo kmardysilofa pragupta uarora.OLD
| |
| − | antmunoz fmaisha kmasarik praroy ugarg
| |
| − | antzhu fmlopez kmbala pratagarwal ukadakia
| |
| − | anurizada fmnoor kmchang pratkumar umoll
| |
| − | anvinod fnieto kmchau priyjain umukherjee
| |
| − | anzaman forabona kmcneil prkkumar upoddar
| |
| − | anzhu fpocaamoros kmfallon prmukhopadhy urasheed
| |
| − | anzzhou frdominguezg kmhayes prouth urehman
| |
| − | aokisamen frhu kmsimon prreddy urosani
| |
| − | apaddayurush frobayobohor kmueller psahu ushafiq
| |
| − | apaddayurush.OLD fsotiropoulo kmungsoo psamang ushassan
| |
| − | apagarwal fuliang kmurgas psangtani usunar
| |
| − | apalit fwelcome kpallmann psekar utegshbayar
| |
| − | apalo fzali kpinzon pshanbhogue utumuluri
| |
| − | apalve gacolella kpipitone pskota uuckun
| |
| − | apamfilie gahuja kprose psmeyer uyevarouskay
| |
| − | aperezantona gakapoor kralbano psokol vachandramou
| |
| − | apettenati gakhan kramcharan psonawane vadabala
| |
| − | aphope galing krayfield psoundarapan vanlin
| |
| − | apilco garrchen krdonaldson pssingh vanugu
| |
| − | apizzulli gashna krisharma psurana vassingh
| |
| − | aplu gatran krjain psutter vbabu
| |
| − | apolanco gaumoithe krkehrli ptitle vbayevskiy
| |
| − | apopoviciu gazzhang krmartin ptonra vbrill
| |
| − | aporripiredd gbalabhadra krokosz ptubiolo vcacciola
| |
| − | aprabhakar gbalazsi krtan puzheng vcarter
| |
| − | apradeep gbangera ksabo pvaishnavi vchanana
| |
| − | aprencis gbermejo ksampathkuma pvaska vduncan
| |
| − | apsinghal gbhattachary kscardigno pvemula verana
| |
| − | apytel gbiselli kschweitzer pvespe vgoel
| |
| − | araghani gbock kshima pximello vhattibettam
| |
| − | arahimyar gbosilca kshou pyao vhegde
| |
| − | arahmati gbrill ksirapu pzbarrett vhnguyen
| |
| − | aranasinghe gchurchill ksoumahoro qiangwang vhuynh
| |
| − | aravula gcma kspuhler qianywu vicdai
| |
| − | arbalasubram gdhama ksucich qiaocwu vidong
| |
| − | arcurtis gdjones kswayze qicao viguo
| |
| − | ardasgupta gduarteramos ktallman qiding vikamat
| |
| − | ardowling geliang kthilanka qihlin villi
| |
| − | areisel gfiakos ktsteven qinie vima
| |
| − | aresnick ggandem ktuzinowski qinjiang vincewu
| |
| − | arfali ggeorgi kuagarwal qinren vinmirandabr
| |
| − | argiannakopo ggopalkrishn kuchan qinzhao vinzheng
| |
| − | arglenn gguleria kumar1 qipan1 visheskumar
| |
| − | arhossain ghe kumar1.OLD qirli vissharma
| |
| − | arjain ghothi kunli qirwu vivlam
| |
| − | arjkrishna gibrown kuraj qxiong viyee
| |
| − | armishra gigill kuzhong raagarwal vjana
| |
| − | arobert gimbriano kveeramah rabasu vjishah
| |
| − | arodriguezd gipark kvshah rachatterjee vkale
| |
| − | arojain girizzo kwahlin rachatterjee.OLD vkhanikaeva
| |
| − | arpahlavan gito kwwalton rachowdhury vkodumurumee
| |
| − | arpbanerjee gjfuentes kwyu raclam vkondipati
| |
| − | arpereira gjiang kwyyoo radsrinivasa vkootagaram
| |
| − | arsaxena gjkim kyadav raggarg vlloyd
| |
| − | arskhan gkementzidis kychao ragte vloganathan
| |
| − | arumar gkowzan kyethiraj rahhuang vlokwani
| |
| − | aryshrivasta glarangeira kylanglois rahraja vmaurya
| |
| − | asadana gmichaels kymjames raich vmontanez
| |
| − | asaji gmihalache kyumin raiislam vpakala
| |
| − | asakhan gmiles kzzhang rairahman vpamula
| |
| − | asamala gmogol lahess rajatkumar vperkowski
| |
| − | asamanta gmoutsanidis lawlin rajdas vranjan
| |
| − | asamavedam gmuradas lbai ramhuang vratnala
| |
| − | asatam gnarh lbozarth ramorosso vrustagi
| |
| − | aschneble gnwood lcaradonna rannadi vseecharan
| |
| − | aschorer goconrosario lchi rapeaning vsnu
| |
| − | ashaalan gparkar lchrastecka rashanbhag vstaub
| |
| − | asharfuddin gperezgonzal lcolleyndeso rashizawa vtangirala
| |
| − | asheneman gprachi lcooke ratwi vvadia
| |
| − | asillato grahme ldavalosalva raychen2 vvedanair
| |
| − | asingal grapacciuolo ldgraham rbaheti vvsharma
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| − | asofianopoul gsbeglia lee104 rbhansali wang113
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| − | asotocambres gshivakumar lee111 rbhowmik wang132
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| − | asrivastava gsuczewski leichen3 rbirnbaum wang159
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| − | bhsiao hotnguyen luzou rochandramoh xichen10
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| − | bighimire hppatil lvasanthakum rodtan xinachen
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| − | bihyu hqaiser lverma roessig xingma
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| − | binnchen hranjan lvotapka rohshukla xingtzhou
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| − | binzhou hridout lwollmuth romjohnson xingyichen
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| − | chen110 jathoffman mhare sbrahmadevar yrhamatzada
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| − | chen147 jaygutierrez mhaziz sbscott ysingh
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| − | chen157 jbak mhorowitz scberg yson
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| − | chen182 jbarrantes miahe schheda yuanjchen
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| − | chen32 jbarron mianchen schiappone yuanzhao
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| − | chen77 jbernauer mibbowman schook yuasong
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| − | chencjiang jbeutel michaliang scokro yuchen4
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| − | chenclu jbhambure michelhuang scsteiger yuchen7
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| − | cheye jbuckley mignatov sdsouza yudding
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| − | chezheng jbuckley.OLD mihur sdssingh yudichen
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| − | chgraham jburzachiell mijia sebramirezvi yuechen4
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| − | chienlee jcespedes mimak seonghjeong yuewang6
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| − | chihhchang jchaillet minghazhang seongioh yuewang7
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| − | chiuyu jchlee mingyli sestoller yuezhao2
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| − | chtian jdcraig mjadhav sfiola yumichen
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| − | chyyoon jecao mkanasani.OLD sgholami yuqiao
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| − | chzuo jefzhong mkapadia sghorashi yushuang
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| − | ckelton jenfu mkonovalyuk sgwilliams yuxlin
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| − | cleeliang jeryeung mkritzer shakislam yuxwu
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| − | clegett jesgoldstein mksanda shalirou yuyguo
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| − | clfischer jeslong mkurakula shanhe yuzhwang
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| − | clongarini jessewang mlaul shanlin2 yyokoi
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| − | clsears jettran mlauterbur shaoliu zafahmad
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| − | cltong jevalle mlcollier shaowang zalseika
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| − | cltucker jeyeung mlng shaqin zariahmed
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| − | cluhmann jeyyoo mlondoo sharinarayan zballard
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| − | clwolfe jfmoon mloverde shawmathew zbhinderwala
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| − | cmack jgaige mmadeira shcchakrabor zcheslog
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| − | cmcarey jgajello mmahboob shclay zcytryn
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| − | cmcgrew jgergen mmahim shdesai zdoora
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| − | cmehndiratta jglazar mmaitra shdixit zdowling
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| − | cmflynn jglimm mmakeev shdixit.OLD zdupont
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| − | cmfoley jgurevitch mmarder shechoi zexizhang
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| − | cmjurgensen jhajagos mmaskaliova shengzhu zeyao
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| − | cmkennedy jharder mmasoumi shengzwang zezhu
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| − | cmoczygemba jheerwig mmatero shenjin zfallon
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| − | cmoote jheinz mmaung sheshao zgrandison
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| − | cmorantesari jheraghty mmcduffie shexiong zgungor
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| − | cmwoo jhjung mmcneill shikgupta zhacai
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| − | cnoe jhollister mmerenstein shilgupta zhage
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| − | cnoutsos jhpark mmilhaven shilliu zhagu
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| − | codlam jiabwang mmimurphy shiltian zhang100
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| − | cohwarner jiachzhu mmursheed shitsai zhang110
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| − | cojiang jiacxu mniznikiewic shivansharma zhang118
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| − | cokeoma jiahuwang mnovotny shivgupta zhang123
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| − | coleary jiajgao moamin shiyuawang zhang133
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| − | conliu jiakwang moewilliams shmmohammed zhang152
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| − | cpercival jialai moflus shmondal zhang173
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| − | cplizio jiamwu mohassan shrajput zhchai
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| − | cprasad jianfeng mojia shroy zhddong
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| − | cqiu jianflin molssi000 shrraman zhedzhang
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| − | crfernandesv jianmtan molssi003 shshekhar.OLD zheng30
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| − | cshiveshwark jiasu molssi008 shubwang zhenqian
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| − | csiebor jiatian molssi009 shuhe zhenwu
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| − | csimmerling jiawang1 molssi010 shujia zhenxliu
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| − | csingleton jiaweichen molssi011 shyyoo zheychen
| |
| − | cstussman jiawezhu molssi012 shyyuan zhezhou1
| |
| − | csyreilly jiaxuyu molssi013 shzzhou zhibwang
| |
| − | cthakur jiayeguo molssi014 siasun zhibyang
| |
| − | ctinker jiayyan molssi015 sichchen zhideng
| |
| − | ctustin jibbai molssi016 sicheliu zhihhe
| |
| − | cuwang jichao molssi017 sichhabra zhihhuang
| |
| − | cvorkas jiddong molssi018 sichliu zhijli
| |
| − | cweistuch jiechen3 molssi019 sigadkar zhimalin
| |
| − | cwoellhof jiemchen molssi020 siggupta zhipxu
| |
| − | cxi jiemzeng molssi021 sihqian zhiwlin
| |
| − | cyanagisawa jienzhu molssi022 sijhuang zhixzhang
| |
| − | cyluo jieyang molssi023 sijjiang zhiye
| |
| − | cyoungflesh jihlin molssi024 sijliu zhke
| |
| − | czhen jihoopark molssi025 silai zhlee
| |
| − | d9wang jihuynh molssi026 singanne zhonliang
| |
| − | dabelinsky jihyepark molssi027 singh4 zhouyu1
| |
| − | dagolden jiikim molssi028 sinhong zhuhli
| |
| − | dagrange jijin molssi029 sinlin zhuxie
| |
| − | daiwang jilao molssi030 sinsmith zhwong
| |
| − | dalpancakmak jiliu1 molssi031 sirle zhxia
| |
| − | damcintyre jimlin molssi032 sishizawa zidiao
| |
| − | damiruddin jimun molssi033 siskhakov ziguan
| |
| − | damoses jin molssi034 siuchan zijiao
| |
| − | dandrew jinghzhou molssi035 siwewang zijizhou
| |
| − | dangelidis jingwenli molssi036 sixliu zikhan
| |
| − | danieliang jingwezhang molssi037 siyadav zilinchen
| |
| − | danitorresra jingwliu molssi038 siyao zilwu
| |
| − | danizheng jinkokim molssi039 siyimaya zirliu
| |
| − | dantorres jinwang2 morahimi siyzou zishao
| |
| − | dantyu jinwei moriasaranib sizahid ziweiwang
| |
| − | danwei jinyhu mozhao sizzheng ziwyu
| |
| − | daoconnell jinyinwang mperess sjaffary zixli
| |
| − | dappark jinyli mpersch sjamshad ziyli
| |
| − | darkow jinyuyang mpetrusky sjeevan ziyozhang
| |
| − | darlin jinyxu mpkatz sjens ziyye
| |
| − | darvind jinzwang mpsantomauro sjiecheng zkrayem
| |
| − | darzeng jiqian mquispecarba sjnelson zlyu
| |
| − | dathanasakos jiychong mradfar sjyang zmou
| |
| − | daultmccoy jiyim mrahimibolda skade zniu
| |
| − | davidlin jiyjung mrakhar skagana zoanderson
| |
| − | davizhao jiyounpark mrashid skalam zoxie
| |
| − | davliang jiyuliu mrathore skalva zqiao
| |
| − | davsilverman jiyuyang mrayeesuddin skann zsongzhu
| |
| − | dawan jjcarter mrehan skapse zuzheng
| |
| − | dawei jjguo mreuter skapur zwray
| |
| − | dawendt jjjones mrichter skarnik zye
| |
| − | dawhu jjnielsen mrius skatariya zzaidi
| |
| − | daxxie jkable mrkumar skavuri zzhuang
| |
| − | dayeung jkiryluk mrosati sketchum zzoya
| |
| − | dayyan jkodner mrsun skobayashi
| |
| − | dayyoon jkohara msardis skogilathota
| |
| − | dbasu jkonopka msavenkov skomatireddy
| |
| − | dbluestein jkottmann msayana skoppuravuri
| |
| − | (base) [ehspector@milan1 home]$ cd ..
| |
| − | (base) [ehspector@milan1 gpfs]$ cd projects/AMS536/
| |
| − | (base) [ehspector@milan1 AMS536]$ ls
| |
| − | 1EVE_Lig_nH.mol2 1eve_Rec_nH.mol2 2018 2021 2024 junk.txt
| |
| − | 1EVE_Lig_wH.mol2 1eve_Rec_wH.mol2 2019 2022 2025 zzz.anchors
| |
| − | 1EVE_Rec_nHDMS.dms 2017 2020 2023 get_anchors.py zzz.programs
| |
| − | (base) [ehspector@milan1 AMS536]$ cd 2025
| |
| − | (base) [ehspector@milan1 2025]$ ls
| |
| − | 1EVE_DOCK_VS INSPH rotations wed_humpday.txt
| |
| − | additional_files robbashrc_file test4.tar
| |
| − | (base) [ehspector@milan1 2025]$ vi test4.tar
| |
| − | (base) [ehspector@milan1 2025]$ pwd
| |
| − | /gpfs/projects/AMS536/2025
| |
| − | (base) [ehspector@milan1 2025]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp /gpfs/projects/AMS536/2025/test4.tar test4.tar
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN test4.tar
| |
| − | (base) [ehspector@milan1 Tutorials]$ mv test4.tar 2w26/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_cartesian_min Notes.txt
| |
| − | 002_surface_spheres 005_rigid 008_rescore test4.tar
| |
| − | 003_gridbox 006_flex_docking commands.txt
| |
| − | (base) [ehspector@milan1 2w26]$ tar -xf test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 005_rigid 008_rescore Notes.txt
| |
| − | 003_gridbox 006_flex_docking 2W26 test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ cd 2W26/
| |
| − | (base) [ehspector@milan1 2W26]$ ls
| |
| − | 001_structure 002_spheres 003_grid 004_dock
| |
| − | (base) [ehspector@milan1 2W26]$ cd 004_dock/
| |
| − | (base) [ehspector@milan1 004_dock]$ ls
| |
| − | 01fps_footprint_scored.txt 01fps_scored.mol2 02rgd.in 03fad.out
| |
| − | 01fps_footprint_scored.txt.pdf 01fps.sh 02rgd.log 03fad_scored.mol2
| |
| − | 01fps_hbond_scored.txt 01min.in 02rgd.out 03fad.sh
| |
| − | 01fps.in 01min.log 02rgd_scored.mol2 04flx.in
| |
| − | 01fps.log1 01min.out 02rgd.sh 04flx.sh
| |
| − | 01fps.log2 01min_scored.mol2 03fad.in old_01min.in
| |
| − | 01fps.out 01min.sh 03fad.log
| |
| − | (base) [ehspector@milan1 004_dock]$ vi 02rgd.in
| |
| − | (base) [ehspector@milan1 004_dock]$ cd ../../
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 005_rigid 008_rescore Notes.txt
| |
| − | 003_gridbox 006_flex_docking 2W26 test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ mv 005_rigid/ 005_dock/
| |
| − | (base) [ehspector@milan1 2w26]$ mv 006_flex_docking/ 006_virtual_screening
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 005_dock 008_rescore Notes.txt
| |
| − | 003_gridbox 006_virtual_screening 2W26 test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ mv 2W26/ Robs_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/02rgd.in 005_dock/
| |
| − | (base) [ehspector@milan1 2w26]$ cd 005_dock/
| |
| − | (base) [ehspector@milan1 005_dock]$ ls
| |
| − | 02rgd.in rigid.in rigid.out_conformers.mol2 rigid.sh
| |
| − | rigid_2.sh rigid.out rigid.out_scored.mol2
| |
| − | (base) [ehspector@milan1 005_dock]$ rm rigid.in
| |
| − | (base) [ehspector@milan1 005_dock]$ mv 02rgd.in rigid.in
| |
| − | (base) [ehspector@milan1 005_dock]$ ls
| |
| − | rigid_2.sh rigid.in rigid.out rigid.out_conformers.mol2 rigid.out_scored.mol2 rigid.sh
| |
| − | (base) [ehspector@milan1 005_dock]$ rm rigid.out_conformers.mol2
| |
| − | (base) [ehspector@milan1 005_dock]$ rm rigid.out_scored.mol2
| |
| − | (base) [ehspector@milan1 005_dock]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 005_dock]$ ls
| |
| − | rigid_2.sh rigid.in rigid.out rigid.sh
| |
| − | (base) [ehspector@milan1 005_dock]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cd 001_structure/
| |
| − | (base) [ehspector@milan1 001_structure]$ la
| |
| − | -bash: la: command not found
| |
| − | (base) [ehspector@milan1 001_structure]$ ls
| |
| − | 2w26_ligand_H_cH.mol2 2w26_protein_H_cH.mol2
| |
| − | 2w26_ligand_noH_nocH.mol2 2w26_protein_noH_nocH.mol2
| |
| − | (base) [ehspector@milan1 001_structure]$ cd ../005_dock/
| |
| − | (base) [ehspector@milan1 005_dock]$ ls
| |
| − | rigid_2.sh rigid.in rigid.out rigid.sh
| |
| − | (base) [ehspector@milan1 005_dock]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 005_dock]$ mkdir rigid_docking
| |
| − | (base) [ehspector@milan1 005_dock]$ mv rigid.in rigid_docking/
| |
| − | (base) [ehspector@milan1 005_dock]$ mv rigid.sh rigid_docking/
| |
| − | (base) [ehspector@milan1 005_dock]$ mv rigid_2.sh rigid_docking/
| |
| − | (base) [ehspector@milan1 005_dock]$ rm rigid.out
| |
| − | (base) [ehspector@milan1 005_dock]$ ls
| |
| − | rigid_docking
| |
| − | (base) [ehspector@milan1 005_dock]$ mkdir flex_docking
| |
| − | (base) [ehspector@milan1 005_dock]$ mkdir_fixed_anchor_docking
| |
| − | -bash: mkdir_fixed_anchor_docking: command not found
| |
| − | (base) [ehspector@milan1 005_dock]$ mkdir fixed_anchor_docking
| |
| − | (base) [ehspector@milan1 005_dock]$ ls
| |
| − | fixed_anchor_docking flex_docking rigid_docking
| |
| − | (base) [ehspector@milan1 005_dock]$ cd rigid_docking/
| |
| − | (base) [ehspector@milan1 rigid_docking]$ ls
| |
| − | rigid_2.sh rigid.in rigid.sh
| |
| − | (base) [ehspector@milan1 rigid_docking]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 rigid_docking]$ vi rigid_2.sh
| |
| − | (base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh
| |
| − | (base) [ehspector@milan1 rigid_docking]$ ls
| |
| − | rigid_2.sh rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh
| |
| − | (base) [ehspector@milan1 rigid_docking]$ vi rigid.out
| |
| − | (base) [ehspector@milan1 rigid_docking]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh
| |
| − | (base) [ehspector@milan1 rigid_docking]$ ls
| |
| − | rigid_2.sh rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh
| |
| − | (base) [ehspector@milan1 rigid_docking]$ vi rigid.out
| |
| − | (base) [ehspector@milan1 rigid_docking]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 rigid_docking]$ bash rigid_2.sh
| |
| − | (base) [ehspector@milan1 rigid_docking]$ ls
| |
| − | rigid_2.sh rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh
| |
| − | (base) [ehspector@milan1 rigid_docking]$ grep -c "Name" rigid_scored.mol2
| |
| − | 7
| |
| − | (base) [ehspector@milan1 rigid_docking]$ cd ..
| |
| − | (base) [ehspector@milan1 005_dock]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_cartesian_min Notes.txt
| |
| − | 002_surface_spheres 005_dock 008_rescore Robs_2w26
| |
| − | 003_gridbox 006_virtual_screening commands.txt test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/03fad.in 005_dock/fixed_anchor_docking/
| |
| − | (base) [ehspector@milan1 2w26]$ cd 005_dock/fixed_anchor_docking/
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ ls
| |
| − | 03fad.in
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ mv 03fad.in fad.in
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ cd ..
| |
| − | (base) [ehspector@milan1 005_dock]$ cp rigid_docking/rigid_2.sh fixed_anchor_docking/fad.sh
| |
| − | (base) [ehspector@milan1 005_dock]$ cd fixed_anchor_docking/
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ ls
| |
| − | fad.in fad.sh
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.in
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.sh
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ bash fad.sh
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ ls
| |
| − | fad.in fad.out fad_scored.mol2 fad.sh
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ vi fad.out
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ cd ..
| |
| − | (base) [ehspector@milan1 005_dock]$ cp fixed_anchor_docking/fad.sh flex_docking/flex.sh
| |
| − | (base) [ehspector@milan1 005_dock]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cp Robs_2w26/004_dock/04flx.in 005_dock/flex_docking/flex.in
| |
| − | (base) [ehspector@milan1 2w26]$ cd 005_dock/flex_docking/
| |
| − | (base) [ehspector@milan1 flex_docking]$ ls
| |
| − | flex.in flex.sh
| |
| − | (base) [ehspector@milan1 flex_docking]$ vi flex.in
| |
| − | (base) [ehspector@milan1 flex_docking]$ vi flex.sh
| |
| − | (base) [ehspector@milan1 flex_docking]$ bash flex.sh
| |
| − | (base) [ehspector@milan1 flex_docking]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan1 flex_docking]$ grep -c "Name" flex_scored.mol2
| |
| − | 20
| |
| − | (base) [ehspector@milan1 flex_docking]$ cd ..
| |
| − | (base) [ehspector@milan1 005_dock]$ cd flex_docking/
| |
| − | (base) [ehspector@milan1 flex_docking]$ pwd
| |
| − | /gpfs/home/ehspector/AMS_536/Tutorials/2w26/005_dock/flex_docking
| |
| − | (base) [ehspector@milan1 flex_docking]$ cd ../fixed_anchor_docking/
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ ls
| |
| − | fad.in fad.out fad_scored.mol2 fad.sh
| |
| − | (base) [ehspector@milan1 fixed_anchor_docking]$ cd ../rigid_docking/
| |
| − | (base) [ehspector@milan1 rigid_docking]$ ls
| |
| − | rigid_2.sh rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh
| |
| − | (base) [ehspector@milan1 rigid_docking]$ cd ../../
| |
| − | (base) [ehspector@milan1 2w26]$ cd ../
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 5EEN/
| |
| − | (base) [ehspector@milan1 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan1 5EEN]$ mv 005_virtual_screen/ 005_dock
| |
| − | (base) [ehspector@milan1 5EEN]$ cd 005_dock/
| |
| − | (base) [ehspector@milan1 005_dock]$ ls
| |
| − | (base) [ehspector@milan1 005_dock]$ mkdir rigid fixed_anchor flex
| |
| − | (base) [ehspector@milan1 005_dock]$ ls
| |
| − | fixed_anchor flex rigid
| |
| − | (base) [ehspector@milan1 005_dock]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/005_dock/rigid_docking/rigid_2.sh 5EEN/005_dock/rigid/
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 5EEN/005_dock/rigid/
| |
| − | (base) [ehspector@milan1 rigid]$ ls
| |
| − | rigid_2.sh
| |
| − | (base) [ehspector@milan1 rigid]$ vi rigid_2.sh
| |
| − | (base) [ehspector@milan1 rigid]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 5EEN
| |
| − | (base) [ehspector@milan2 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan2 5EEN]$ cd 005_dock/
| |
| − | (base) [ehspector@milan2 005_dock]$ ls
| |
| − | fixed_anchor flex rigid
| |
| − | (base) [ehspector@milan2 005_dock]$ cd rigid/
| |
| − | (base) [ehspector@milan2 rigid]$ ls
| |
| − | rigid_2.sh
| |
| − | (base) [ehspector@milan2 rigid]$ touch rigid.in
| |
| − | (base) [ehspector@milan2 rigid]$ vi rigid_2.sh
| |
| − | (base) [ehspector@milan2 rigid]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i rigid.in
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):rigid
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy [yes] (yes no):
| |
| − | internal_energy_rep_exp [12] ():
| |
| − | internal_energy_cutoff [100.0] ():
| |
| − | Note: Internal energy only includes repulsive VDW for growth and/or minimization.
| |
| − |
| |
| − | Molecule Library Input Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_atom_file [database.mol2] ():5EEN.lig.min_scored.mol2
| |
| − | limit_max_ligands [no] (yes no):
| |
| − | skip_molecule [no] (yes no):
| |
| − | read_mol_solvation [no] (yes no):
| |
| − | calculate_rmsd [no] (yes no):yes
| |
| − | use_rmsd_reference_mol [no] (yes no):yes
| |
| − | rmsd_reference_filename [ligand_rmsd.mol2] ():5EEN.lig.min_scored.mol2
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter [no] (yes no):
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand [yes] (yes no):
| |
| − | automated_matching [yes] (yes no):
| |
| − | receptor_site_file [receptor.sph] ():../../002_surface_spheres/selected_spheres.sph
| |
| − | max_orientations [1000] ():
| |
| − | critical_points [no] (yes no):
| |
| − | chemical_matching [no] (yes no):
| |
| − | use_ligand_spheres [no] (yes no):
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter [no] (yes no):
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules [yes] (yes no):
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary [no] (yes no):
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary [yes] (yes no):
| |
| − | grid_score_rep_rad_scale [1] ():
| |
| − | grid_score_vdw_scale [1] ():
| |
| − | grid_score_es_scale [1] ():
| |
| − | grid_lig_efficiency [no] (yes no):
| |
| − | grid_score_grid_prefix [grid] ():../../003_gridbox/grid
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand [yes] (yes no):yes
| |
| − | simplex_max_iterations [1000] ():
| |
| − | simplex_tors_premin_iterations [0] ():
| |
| − | simplex_max_cycles [1] ():
| |
| − | simplex_score_converge [0.1] ():
| |
| − | simplex_cycle_converge [1.0] ():
| |
| − | simplex_trans_step [1.0] ():
| |
| − | simplex_rot_step [0.1] ():
| |
| − | simplex_tors_step [10.0] ():
| |
| − | simplex_final_min [no] (yes no):
| |
| − | simplex_random_seed [0] ():
| |
| − | simplex_restraint_min [no] (yes no):
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model [all] (all | united):
| |
| − | vdw_defn_file [vdw.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
| |
| − | flex_defn_file [flex.defn] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
| |
| − | flex_drive_file [flex_drive.tbl] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
| |
| − |
| |
| − | Molecule Library Output Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_outfile_prefix [output] ():rigid
| |
| − | write_mol_solvation [no] (yes no):
| |
| − | write_orientations [no] (yes no):
| |
| − | num_scored_conformers [1] ():
| |
| − | score_threshold [100.0] ():
| |
| − | rank_ligands [no] (yes no):
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | Initializing Library File Routines...
| |
| − |
| |
| − |
| |
| − |
| |
| − | Could not open 5EEN.lig.min_scored.mol2 for reading. Program will terminate.
| |
| − |
| |
| − | (base) [ehspector@milan2 rigid]$ cd ../../004_energymin/
| |
| − | (base) [ehspector@milan2 004_energymin]$ ls
| |
| − | 5een.lig.min_scored.mol2 min.in min.out min.sh
| |
| − | (base) [ehspector@milan2 004_energymin]$ cd ../005_dock/rigid/
| |
| − | (base) [ehspector@milan2 rigid]$ ls
| |
| − | rigid_2.sh rigid.in
| |
| − | (base) [ehspector@milan2 rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan2 rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan2 rigid]$ bash rigid_2.sh
| |
| − | (base) [ehspector@milan2 rigid]$ ls
| |
| − | rigid_2.sh rigid.in rigid.out
| |
| − | (base) [ehspector@milan2 rigid]$ vi rigid.out
| |
| − | (base) [ehspector@milan2 rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan2 rigid]$ bash rigid_2.sh
| |
| − | (base) [ehspector@milan2 rigid]$ ls
| |
| − | rigid_2.sh rigid.in rigid.out rigid_scored.mol2
| |
| − | (base) [ehspector@milan2 rigid]$ vi rigid.out
| |
| − | (base) [ehspector@milan2 rigid]$ cd ..
| |
| − | (base) [ehspector@milan2 005_dock]$ cd ..
| |
| − | (base) [ehspector@milan2 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/rigid/
| |
| − | (base) [ehspector@milan2 rigid]$ rm rigid.in
| |
| − | (base) [ehspector@milan2 rigid]$ cd ..
| |
| − | (base) [ehspector@milan2 005_dock]$ cd ..
| |
| − | (base) [ehspector@milan2 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/rigid_docking/rigid.in 5EEN/005_dock/rigid/rigid.in
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/rigid/
| |
| − | (base) [ehspector@milan2 rigid]$ ls
| |
| − | rigid_2.sh rigid.in rigid.out rigid_scored.mol2
| |
| − | (base) [ehspector@milan2 rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan2 rigid]$ bash rigid_2.sh
| |
| − | (base) [ehspector@milan2 rigid]$ ls
| |
| − | rigid_2.sh rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2
| |
| − | (base) [ehspector@milan2 rigid]$ grep -c "Name" rigid_scored.mol2
| |
| − | 19
| |
| − | (base) [ehspector@milan2 rigid]$ cd ..
| |
| − | (base) [ehspector@milan2 005_dock]$ cd ..
| |
| − | (base) [ehspector@milan2 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/fixed_anchor_docking/fad.in 5EEN/005_dock/fixed_anchor/fad.in
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/fixed_anchor_docking/fad.sh 5EEN/005_dock/fixed_anchor/fad.sh
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/fixed_anchor/
| |
| − | (base) [ehspector@milan2 fixed_anchor]$ ls
| |
| − | fad.in fad.sh
| |
| − | (base) [ehspector@milan2 fixed_anchor]$ vi fad.in
| |
| − | (base) [ehspector@milan2 fixed_anchor]$ vi fad.sh
| |
| − | (base) [ehspector@milan2 fixed_anchor]$ bash fad.sh
| |
| − | (base) [ehspector@milan2 fixed_anchor]$ ls
| |
| − | fad.in fad.out fad_scored.mol2 fad.sh
| |
| − | (base) [ehspector@milan2 fixed_anchor]$ grep -c "Name" fad_scored.mol2
| |
| − | 7
| |
| − | (base) [ehspector@milan2 fixed_anchor]$ cd ..
| |
| − | (base) [ehspector@milan2 005_dock]$ cd ..
| |
| − | (base) [ehspector@milan2 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/flex_docking/flex.in 5EEN/005_dock/flex/flex.in
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 2w26/005_dock/flex_docking/flex.sh 5EEN/005_dock/flex/flex.sh
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex.in flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ vi flex.in
| |
| − | (base) [ehspector@milan2 flex]$ bash flex.sh
| |
| − | exit
| |
| − | (base) [ehspector@milan2 flex]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ grep -c "Name" flex_scored.mol2
| |
| − | 3
| |
| − | (base) [ehspector@milan2 flex]$ vi flex.out
| |
| − | (base) [ehspector@milan2 flex]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ rm flex.out
| |
| − | (base) [ehspector@milan2 flex]$ bash flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ vi flex.
| |
| − | (base) [ehspector@milan2 flex]$ vi flex.out
| |
| − | (base) [ehspector@milan2 flex]$ cd ..
| |
| − | (base) [ehspector@milan2 005_dock]$ ls
| |
| − | fixed_anchor flex rigid
| |
| − | (base) [ehspector@milan2 005_dock]$ cd flex/
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ cd ..
| |
| − | (base) [ehspector@milan2 005_dock]$ cd ..
| |
| − | (base) [ehspector@milan2 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/
| |
| − | (base) [ehspector@milan2 1O86]$ ls
| |
| − | 001_structure 003_gridbox 005_virtual_screen 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan2 1O86]$ mv 005_virtual_screen/ 005_dock
| |
| − | (base) [ehspector@milan2 1O86]$ cd 005_dock/
| |
| − | (base) [ehspector@milan2 005_dock]$ mkdir rigid fixed_anchor flex
| |
| − | (base) [ehspector@milan2 005_dock]$ cd ../../
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid.in 1O86/005_dock/rigid/rigin.in
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid.sh 1O86/005_dock/rigid/rigin.sh
| |
| − | cp: cannot stat '5EEN/005_dock/rigid/rigid.sh': No such file or directory
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 5EEN/005_dock/rigid/rigid_2.sh 1O86/005_dock/rigid/rigin.sh
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/005_dock/rigid/
| |
| − | (base) [ehspector@milan2 rigid]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP AMS_548 % cd ../AMS_691
| |
| − | (base) supremestudier@Evans-MBP AMS_691 % ls
| |
| − | AMS691_01.pdf Lectures Projects Text_book
| |
| − | (base) supremestudier@Evans-MBP AMS_691 % mkdir PyTorch
| |
| − | (base) supremestudier@Evans-MBP AMS_691 % cd ../AMS_536
| |
| − | (base) supremestudier@Evans-MBP AMS_536 % ls
| |
| − | Tutorial project.example.dGhyd.pdf
| |
| − | project.example.MMPS.pdf zzz_2025_01_29a_seawulf_notes.docx
| |
| − | (base) supremestudier@Evans-MBP AMS_536 % cd Tutorial
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ls
| |
| − | 1O86 2w26 5EEN folders.txt
| |
| − | (base) supremestudier@Evans-MBP Tutorial % cd 5EEN
| |
| − | (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ cd 1O86/005_dock/rigid/
| |
| − | -bash: cd: 1O86/005_dock/rigid/: No such file or directory
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd 1O86/005_dock/rigid/
| |
| − | -bash: cd: 1O86/005_dock/rigid/: No such file or directory
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 1O86/005_dock/rigid/
| |
| − | (base) [ehspector@milan1 rigid]$ ls
| |
| − | rigin.in rigin.sh
| |
| − | (base) [ehspector@milan1 rigid]$ mv rigin.in rigid.in
| |
| − | (base) [ehspector@milan1 rigid]$ mv rigin.sh rigid.sh
| |
| − | (base) [ehspector@milan1 rigid]$ vi rigid.in
| |
| − | (base) [ehspector@milan1 rigid]$ cd ../../004_energymin/
| |
| − | (base) [ehspector@milan1 004_energymin]$ ls
| |
| − | 1O86.lig.min_scored.mol2 min.in min.out min.sh
| |
| − | (base) [ehspector@milan1 004_energymin]$ cd ../005_dock/rigid/
| |
| − | (base) [ehspector@milan1 rigid]$ ls
| |
| − | rigid.in rigid.sh
| |
| − | (base) [ehspector@milan1 rigid]$ vi rigid.sh
| |
| − | (base) [ehspector@milan1 rigid]$ bash rigid.sh
| |
| − | (base) [ehspector@milan1 rigid]$ ls
| |
| − | rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh
| |
| − | (base) [ehspector@milan1 rigid]$ vi rigid.out
| |
| − | (base) [ehspector@milan1 rigid]$ grep -c "Name" rigid_scored.mol2
| |
| − | 7
| |
| − | (base) [ehspector@milan1 rigid]$ cd ..
| |
| − | (base) [ehspector@milan1 005_dock]$ cd ../../
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/fixed_anchor/fad.in 1O86/005_dock/fixed_anchor/fad.in
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/fixed_anchor/fad.sh 1O86/005_dock/fixed_anchor/fad.sh
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/flex/flex.in 1O86/005_dock/flex/flex.in
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 5EEN/005_dock/flex/flex.sh 1O86/005_dock/flex/flex.sh
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 1O86/005_dock/fixed_anchor/
| |
| − | (base) [ehspector@milan1 fixed_anchor]$ ls
| |
| − | fad.in fad.sh
| |
| − | (base) [ehspector@milan1 fixed_anchor]$ vi fad.in
| |
| − | (base) [ehspector@milan1 fixed_anchor]$ bash fad.sh
| |
| − | (base) [ehspector@milan1 fixed_anchor]$ cd ..
| |
| − | (base) [ehspector@milan1 005_dock]$ cd fixed_anchor/
| |
| − | (base) [ehspector@milan1 fixed_anchor]$ ls
| |
| − | fad.in fad.out fad_scored.mol2 fad.sh
| |
| − | (base) [ehspector@milan1 fixed_anchor]$ grep -c "Name" fad_scored.mol2
| |
| − | 3
| |
| − | (base) [ehspector@milan1 fixed_anchor]$ cd ..
| |
| − | (base) [ehspector@milan1 005_dock]$ cd flex/
| |
| − | (base) [ehspector@milan1 flex]$ ls
| |
| − | flex.in flex.sh
| |
| − | (base) [ehspector@milan1 flex]$ vi flex.in
| |
| − | (base) [ehspector@milan1 flex]$ bash flex.sh
| |
| − | ^C^X
| |
| − | (base) [ehspector@milan1 flex]$ vi flex.in
| |
| − | (base) [ehspector@milan1 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan1 flex]$ rm flex.out
| |
| − | (base) [ehspector@milan1 flex]$ bash flex.sh
| |
| − | (base) [ehspector@milan1 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan1 flex]$ vi flex.out
| |
| − | (base) [ehspector@milan1 flex]$ grep -c "Name" flex_scored.mol2
| |
| − | 32
| |
| − | (base) [ehspector@milan1 flex]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/005_dock/flex_docking/
| |
| − | (base) [ehspector@milan1 flex_docking]$ vi flex.in
| |
| − | (base) [ehspector@milan1 flex_docking]$ cd ..
| |
| − | (base) [ehspector@milan1 005_dock]$ cd ../../5EEN/005_dock/flex/
| |
| − | (base) [ehspector@milan1 flex]$ vi flex.in
| |
| − | (base) [ehspector@milan1 flex]$ exit
| |
| − | (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | ****IMPORTANT MESSAGE BELOW****
| |
| − |
| |
| − |
| |
| − | In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.
| |
| − |
| |
| − | (base) [ehspector@login2 ~]$ home
| |
| − | (base) [ehspector@login2 espector]$ cd builds/alpha_branch/install/
| |
| − | (base) [ehspector@login2 install]$ ls
| |
| − | bluegenel gnu.acml homebrew intel.mkl sgi
| |
| − | bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel
| |
| − | config.h gnu.parallel ibmaix Makefile test
| |
| − | configure gnu.parallel.rdkit intel oneapi
| |
| − | docker gnu.rdkit intel.intelmpi.parallel pgi
| |
| − | gnu gnu.valgrind intel.ip.mkl rules.h
| |
| − | (base) [ehspector@login2 install]$ ./configure gnu
| |
| − | The requested configuration file was found.
| |
| − |
| |
| − | Warning: the configuration file already exists with the creation stamp:
| |
| − | # Created at Mon Jan 20 04:34:02 PM EST 2025 via ./configure gnu.rdkit
| |
| − | It will be overwritten !
| |
| − |
| |
| − | Don't forget to make clean before rebuilding.
| |
| − | To reconfigure and rebuild everything start with make -i distclean:
| |
| − | Reconfiguring after make -i distclean will avoid this warning.
| |
| − |
| |
| − | The DOCK configuration file has been created.
| |
| − | (base) [ehspector@login2 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@login2 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Wed Feb 12 10:29:40 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dock.o dock.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp
| |
| − | g++ -c -O2 -std=c++11 -o filter.o filter.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp
| |
| − | g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp
| |
| − | g++ -c -O2 -std=c++11 -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp
| |
| − | g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp
| |
| − | g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o orient.o orient.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score.o score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp
| |
| − | g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp
| |
| − | g++ -c -O2 -std=c++11 -o trace.o trace.cpp
| |
| − | g++ -c -O2 -std=c++11 -o utils.o utils.cpp
| |
| − | g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp
| |
| − | g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp
| |
| − | cd nab && make all
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | gcc -c -O3 -D_ANSI_SOURCE molio.c
| |
| − | gcc -c -O2 -o prm.o prm.c
| |
| − | make is_LEX_available
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c
| |
| − | gcc -c -O2 -o traceback.o traceback.c
| |
| − | gcc -c -O2 -o select_atoms.o select_atoms.c
| |
| − | gcc -c -O2 -o memutil.o memutil.c
| |
| − | gcc -c -O2 -o reslib.o reslib.c
| |
| − | gcc -c -O2 -o jacobi.o jacobi.c
| |
| − | gcc -c -O2 -o molutil.o molutil.c
| |
| − | gcc -c -O2 -o chirvol.o chirvol.c
| |
| − | gcc -c -O2 -o regexp.o regexp.c
| |
| − | gcc -c -O2 -o binpos.o binpos.c
| |
| − | gcc -c -O2 -o time.o time.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE rand2.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE conjgrad.c
| |
| − | gcc -c -O2 -o database.o database.c
| |
| − | gcc -c -O2 -o tleap.o tleap.c
| |
| − | ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
| |
| − | ar: creating nab.a
| |
| − | a - molio.o
| |
| − | a - prm.o
| |
| − | a - sff.o
| |
| − | a - traceback.o
| |
| − | a - select_atoms.o
| |
| − | a - memutil.o
| |
| − | a - reslib.o
| |
| − | a - jacobi.o
| |
| − | a - molutil.o
| |
| − | a - chirvol.o
| |
| − | a - regexp.o
| |
| − | a - binpos.o
| |
| − | a - time.o
| |
| − | a - rand2.o
| |
| − | a - conjgrad.o
| |
| − | a - database.o
| |
| − | a - tleap.o
| |
| − | ranlib nab.a
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
| |
| − | ar cr libgzstream.a gzstream.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
| |
| − | -lm -lpthread
| |
| − | mv dock6 ../../bin
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − |
| |
| − | Installation of
| |
| − | DOCK v6.12
| |
| − | program dock is complete at Wed Feb 12 10:31:34 EST 2025.
| |
| − |
| |
| − | (base) [ehspector@login2 install]$ cd ..
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd src/dock
| |
| − | (base) [ehspector@login2 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@login2 dock]$ cd ..
| |
| − | (base) [ehspector@login2 src]$ cd ../install/
| |
| − | (base) [ehspector@login2 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@login2 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Wed Feb 12 10:33:23 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dock.o dock.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2_retain(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:550:9: error: ‘num_zeros’ was not declared in this scope
| |
| − | 550 | if (num_zeros == mol.num_atoms){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | make[1]: *** [dockmol.o] Error 1
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [dock] Error 2
| |
| − | (base) [ehspector@login2 install]$ cd ..
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd src/dock
| |
| − | (base) [ehspector@login2 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@login2 dock]$ cd ../
| |
| − | (base) [ehspector@login2 src]$ cd ../install/
| |
| − | (base) [ehspector@login2 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@login2 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Wed Feb 12 10:36:16 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dock.o dock.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp
| |
| − | g++ -c -O2 -std=c++11 -o filter.o filter.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp
| |
| − | g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp
| |
| − | g++ -c -O2 -std=c++11 -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp
| |
| − | g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp
| |
| − | g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o orient.o orient.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score.o score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp
| |
| − | g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp
| |
| − | g++ -c -O2 -std=c++11 -o trace.o trace.cpp
| |
| − | g++ -c -O2 -std=c++11 -o utils.o utils.cpp
| |
| − | g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp
| |
| − | g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp
| |
| − | cd nab && make all
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | gcc -c -O3 -D_ANSI_SOURCE molio.c
| |
| − | gcc -c -O2 -o prm.o prm.c
| |
| − | make is_LEX_available
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c
| |
| − | gcc -c -O2 -o traceback.o traceback.c
| |
| − | gcc -c -O2 -o select_atoms.o select_atoms.c
| |
| − | gcc -c -O2 -o memutil.o memutil.c
| |
| − | gcc -c -O2 -o reslib.o reslib.c
| |
| − | gcc -c -O2 -o jacobi.o jacobi.c
| |
| − | gcc -c -O2 -o molutil.o molutil.c
| |
| − | gcc -c -O2 -o chirvol.o chirvol.c
| |
| − | gcc -c -O2 -o regexp.o regexp.c
| |
| − | gcc -c -O2 -o binpos.o binpos.c
| |
| − | gcc -c -O2 -o time.o time.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE rand2.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE conjgrad.c
| |
| − | gcc -c -O2 -o database.o database.c
| |
| − | gcc -c -O2 -o tleap.o tleap.c
| |
| − | ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
| |
| − | ar: creating nab.a
| |
| − | a - molio.o
| |
| − | a - prm.o
| |
| − | a - sff.o
| |
| − | a - traceback.o
| |
| − | a - select_atoms.o
| |
| − | a - memutil.o
| |
| − | a - reslib.o
| |
| − | a - jacobi.o
| |
| − | a - molutil.o
| |
| − | a - chirvol.o
| |
| − | a - regexp.o
| |
| − | a - binpos.o
| |
| − | a - time.o
| |
| − | a - rand2.o
| |
| − | a - conjgrad.o
| |
| − | a - database.o
| |
| − | a - tleap.o
| |
| − | ranlib nab.a
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
| |
| − | ar cr libgzstream.a gzstream.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
| |
| − | -lm -lpthread
| |
| − | mv dock6 ../../bin
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − |
| |
| − | Installation of
| |
| − | DOCK v6.12
| |
| − | program dock is complete at Wed Feb 12 10:38:00 EST 2025.
| |
| − |
| |
| − | (base) [ehspector@login2 install]$ cd ..
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd ,,
| |
| − | -bash: cd: ,,: No such file or directory
| |
| − | (base) [ehspector@login2 alpha_branch]$ home
| |
| − | (base) [ehspector@login2 espector]$ cd 4s0v/gas_teiger/
| |
| − | (base) [ehspector@login2 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_4.in gas.in no_gas.out_scored.mol2
| |
| − | 1AAQ_yesG.mol2 gas_4.out gas.out test.mol2
| |
| − | gas_2.in gas_4.out_scored.mol2 gas.out_scored.mol2 test_nocharge.mol2
| |
| − | gas_2.out gas_5.in no_charge
| |
| − | gas_3.in gas_5.out no_gas.in
| |
| − | gas_3.out gas_5.out_scored.mol2 no_gas.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_4.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ rm gas_4.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.out gas_5.out_scored.mol2 no_gas.in
| |
| − | 1AAQ_yesG.mol2 gas_4.in gas.in no_gas.out
| |
| − | gas_2.in gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2
| |
| − | gas_2.out gas_5.in gas.out_scored.mol2 test.mol2
| |
| − | gas_3.in gas_5.out no_charge test_nocharge.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_4.out_scored.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_4.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_4.in
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi 1AAQ_noG.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_4.in
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_5.in
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi 1AAQ_noG.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi 1AAQ_yesG.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ dock6 -i gas_5.in -o gas_5.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.out gas_5.out_scored.mol2 no_gas.in
| |
| − | 1AAQ_yesG.mol2 gas_4.in gas.in no_gas.out
| |
| − | gas_2.in gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2
| |
| − | gas_2.out gas_5.in gas.out_scored.mol2 test.mol2
| |
| − | gas_3.in gas_5.out no_charge test_nocharge.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_5.out_scored.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi 1AAQ_yesG.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_5.in
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_4.in
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_4.in
| |
| − | (base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_4.in gas.in no_gas.out_scored.mol2
| |
| − | 1AAQ_yesG.mol2 gas_4.out gas.out test.mol2
| |
| − | gas_2.in gas_4.out_scored.mol2 gas.out_scored.mol2 test_nocharge.mol2
| |
| − | gas_2.out gas_5.in no_charge
| |
| − | gas_3.in gas_5.out no_gas.in
| |
| − | gas_3.out gas_5.out_scored.mol2 no_gas.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_4.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@login2 4s0v]$ cd ..
| |
| − | (base) [ehspector@login2 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@login2 espector]$ cd builds/alpha_branch/src/dock
| |
| − | (base) [ehspector@login2 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@login2 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@login2 dock]$ cd ..
| |
| − | (base) [ehspector@login2 src]$ cd ../install/
| |
| − | (base) [ehspector@login2 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@login2 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Wed Feb 12 10:49:54 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dock.o dock.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2_retain(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:542:5: error: ‘If’ was not declared in this scope
| |
| − | 542 | If all partial charges are zero, it is a bad molecule
| |
| − | | ^~
| |
| − | dockmol.cpp:546:13: error: ‘num_zeros’ was not declared in this scope
| |
| − | 546 | num_zeros += 1;
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp:549:6: error: ‘Is’ was not declared in this scope
| |
| − | 549 | Is it a bad molecule?
| |
| − | | ^~
| |
| − | dockmol.cpp:552:7: error: ‘else’ without a previous ‘if’
| |
| − | 552 | } else {
| |
| − | | ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | make[1]: *** [dockmol.o] Error 1
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [dock] Error 2
| |
| − | (base) [ehspector@login2 install]$ cd ../src/dock
| |
| − | (base) [ehspector@login2 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@login2 dock]$ cd ..
| |
| − | (base) [ehspector@login2 src]$ cd ..
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd src/dock
| |
| − | (base) [ehspector@login2 dock]$ cd ../../
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@login2 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@login2 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Wed Feb 12 10:52:33 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dock.o dock.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp
| |
| − | g++ -c -O2 -std=c++11 -o filter.o filter.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp
| |
| − | g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp
| |
| − | g++ -c -O2 -std=c++11 -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp
| |
| − | g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp
| |
| − | g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o orient.o orient.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score.o score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp
| |
| − | g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp
| |
| − | g++ -c -O2 -std=c++11 -o trace.o trace.cpp
| |
| − | g++ -c -O2 -std=c++11 -o utils.o utils.cpp
| |
| − | g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp
| |
| − | g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp
| |
| − | cd nab && make all
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | gcc -c -O3 -D_ANSI_SOURCE molio.c
| |
| − | gcc -c -O2 -o prm.o prm.c
| |
| − | make is_LEX_available
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c
| |
| − | gcc -c -O2 -o traceback.o traceback.c
| |
| − | gcc -c -O2 -o select_atoms.o select_atoms.c
| |
| − | gcc -c -O2 -o memutil.o memutil.c
| |
| − | gcc -c -O2 -o reslib.o reslib.c
| |
| − | gcc -c -O2 -o jacobi.o jacobi.c
| |
| − | gcc -c -O2 -o molutil.o molutil.c
| |
| − | gcc -c -O2 -o chirvol.o chirvol.c
| |
| − | gcc -c -O2 -o regexp.o regexp.c
| |
| − | gcc -c -O2 -o binpos.o binpos.c
| |
| − | gcc -c -O2 -o time.o time.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE rand2.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE conjgrad.c
| |
| − | gcc -c -O2 -o database.o database.c
| |
| − | gcc -c -O2 -o tleap.o tleap.c
| |
| − | ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
| |
| − | ar: creating nab.a
| |
| − | a - molio.o
| |
| − | a - prm.o
| |
| − | a - sff.o
| |
| − | a - traceback.o
| |
| − | a - select_atoms.o
| |
| − | a - memutil.o
| |
| − | a - reslib.o
| |
| − | a - jacobi.o
| |
| − | a - molutil.o
| |
| − | a - chirvol.o
| |
| − | a - regexp.o
| |
| − | a - binpos.o
| |
| − | a - time.o
| |
| − | a - rand2.o
| |
| − | a - conjgrad.o
| |
| − | a - database.o
| |
| − | a - tleap.o
| |
| − | ranlib nab.a
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
| |
| − | ar cr libgzstream.a gzstream.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
| |
| − | -lm -lpthread
| |
| − | mv dock6 ../../bin
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − |
| |
| − | Installation of
| |
| − | DOCK v6.12
| |
| − | program dock is complete at Wed Feb 12 10:54:21 EST 2025.
| |
| − |
| |
| − | (base) [ehspector@login2 install]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | ****IMPORTANT MESSAGE BELOW****
| |
| − |
| |
| − |
| |
| − | In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.
| |
| − |
| |
| − | (base) [ehspector@login1 ~]$ home
| |
| − | (base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
| |
| − | (base) [ehspector@login1 src]$ ls
| |
| − | accessories antechamber dock docktools gbsa_grids grid Makefile mopac6 rdkit resp tleap
| |
| − | (base) [ehspector@login1 src]$ cd dock
| |
| − | (base) [ehspector@login1 dock]$ ls
| |
| − | amber_typer.cpp defreal.h iso_align.o README score.o
| |
| − | amber_typer.h dock.cpp library_file.cpp sasa.cpp score_ph4.cpp
| |
| − | amber_typer.o dockmol.cpp library_file.h sasa.h score_ph4.h
| |
| − | base_grid.cpp dockmol.h library_file.o sasa.o score_ph4.o
| |
| − | base_grid.h dockmol.o limit_max_change.cpp score_amber.cpp score_sasa.cpp
| |
| − | base_grid.o dock.o limit_max_change.h score_amber.h score_sasa.h
| |
| − | base_mpi.cpp filter.cpp limit_max_change.o score_amber.o score_sasa.o
| |
| − | base_mpi.h filter.h lol score_chemgrid.cpp score_solvent.cpp
| |
| − | base_mpi.o filter.o Makefile score_chemgrid.h score_solvent.h
| |
| − | base_score.cpp fingerprint.cpp master_conf.cpp score_chemgrid.o score_solvent.o
| |
| − | base_score.h fingerprint.h master_conf.h score.cpp score_volume.cpp
| |
| − | base_score.o fingerprint.o master_conf.o score_descriptor.cpp score_volume.h
| |
| − | conf_gen_ag.cpp fraggraph.cpp master_score.cpp score_descriptor.h score_volume.o
| |
| − | conf_gen_ag.h fraggraph.h master_score.h score_descriptor.o simplex.cpp
| |
| − | conf_gen_ag.o fraggraph.o master_score.o score_footprint.cpp simplex.h
| |
| − | conf_gen_cg.cpp fragment.cpp mem_info.cpp score_footprint.h simplex.o
| |
| − | conf_gen_cg.h fragment.h mem_info.h score_footprint.o sphere.cpp
| |
| − | conf_gen_cg.o fragment.o mem_info.o score_gist.cpp sphere.h
| |
| − | conf_gen_dn.cpp gasteiger.cpp nab score_gist.h sphere.o
| |
| − | conf_gen_dn_ga.cpp gasteiger.h nabcode.h score_gist.o tnt
| |
| − | conf_gen_dn_ga.h gasteiger.o nab.h score.h trace.cpp
| |
| − | conf_gen_dn_ga.o grid.cpp orient.cpp score_hbond.cpp trace.h
| |
| − | conf_gen_dn.h grid.h orient.h score_hbond.h trace.inl
| |
| − | conf_gen_dn.o grid.o orient.o score_hbond.o trace.o
| |
| − | conf_gen_ga.cpp gzstream rddrive.cpp score_internal.cpp utils.cpp
| |
| − | conf_gen_ga.h hungarian.cpp rddrive.h score_internal.h utils.h
| |
| − | conf_gen_ga.o hungarian.h rddrive.o score_internal.o utils.o
| |
| − | conf_gen_hdb.cpp hungarian.o rdtyper.cpp score_multigrid.cpp version.h
| |
| − | conf_gen_hdb.h iso_align.cpp rdtyper.h score_multigrid.h xlogp.cpp
| |
| − | conf_gen_hdb.o iso_align.h rdtyper.o score_multigrid.o xlogp.h
| |
| − | (base) [ehspector@login1 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@login1 dock]$ cd ../../install/
| |
| − | (base) [ehspector@login1 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@login1 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Wed Feb 12 13:24:37 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dock.o dock.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp
| |
| − | g++ -c -O2 -std=c++11 -o filter.o filter.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp
| |
| − | g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp
| |
| − | g++ -c -O2 -std=c++11 -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp
| |
| − | g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp
| |
| − | g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o orient.o orient.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score.o score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp
| |
| − | g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp
| |
| − | g++ -c -O2 -std=c++11 -o trace.o trace.cpp
| |
| − | g++ -c -O2 -std=c++11 -o utils.o utils.cpp
| |
| − | g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp
| |
| − | g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp
| |
| − | cd nab && make all
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | gcc -c -O3 -D_ANSI_SOURCE molio.c
| |
| − | gcc -c -O2 -o prm.o prm.c
| |
| − | make is_LEX_available
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c
| |
| − | gcc -c -O2 -o traceback.o traceback.c
| |
| − | gcc -c -O2 -o select_atoms.o select_atoms.c
| |
| − | gcc -c -O2 -o memutil.o memutil.c
| |
| − | gcc -c -O2 -o reslib.o reslib.c
| |
| − | gcc -c -O2 -o jacobi.o jacobi.c
| |
| − | gcc -c -O2 -o molutil.o molutil.c
| |
| − | gcc -c -O2 -o chirvol.o chirvol.c
| |
| − | gcc -c -O2 -o regexp.o regexp.c
| |
| − | gcc -c -O2 -o binpos.o binpos.c
| |
| − | gcc -c -O2 -o time.o time.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE rand2.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE conjgrad.c
| |
| − | gcc -c -O2 -o database.o database.c
| |
| − | gcc -c -O2 -o tleap.o tleap.c
| |
| − | ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
| |
| − | ar: creating nab.a
| |
| − | a - molio.o
| |
| − | a - prm.o
| |
| − | a - sff.o
| |
| − | a - traceback.o
| |
| − | a - select_atoms.o
| |
| − | a - memutil.o
| |
| − | a - reslib.o
| |
| − | a - jacobi.o
| |
| − | a - molutil.o
| |
| − | a - chirvol.o
| |
| − | a - regexp.o
| |
| − | a - binpos.o
| |
| − | a - time.o
| |
| − | a - rand2.o
| |
| − | a - conjgrad.o
| |
| − | a - database.o
| |
| − | a - tleap.o
| |
| − | ranlib nab.a
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
| |
| − | ar cr libgzstream.a gzstream.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
| |
| − | -lm -lpthread
| |
| − | mv dock6 ../../bin
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − |
| |
| − | Installation of
| |
| − | DOCK v6.12
| |
| − | program dock is complete at Wed Feb 12 13:27:09 EST 2025.
| |
| − |
| |
| − | (base) [ehspector@login1 install]$ cd ..
| |
| − | (base) [ehspector@login1 alpha_branch]$ cd ../../4s0v/gas_teiger/
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.out gas_5.out no_charge test_nocharge.mol2
| |
| − | 1AAQ_yesG.mol2 gas_4.in gas_5.out_scored.mol2 no_gas.in
| |
| − | gas_2.in gas_4.out gas.in no_gas.out
| |
| − | gas_2.out gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2
| |
| − | gas_3.in gas_5.in gas.out_scored.mol2 test.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas_4.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.out gas_5.out no_charge test_nocharge.mol2
| |
| − | 1AAQ_yesG.mol2 gas_4.in gas_5.out_scored.mol2 no_gas.in
| |
| − | gas_2.in gas_4.out gas.in no_gas.out
| |
| − | gas_2.out gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2
| |
| − | gas_3.in gas_5.in gas.out_scored.mol2 test.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi 1AAQ_noG.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas_4.out_scored.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas_3.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi test_nocharge.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas_3.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas_3.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ dock6 -i gas_3.in -o gas_3.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas_3.out_scored.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi test_nocharge.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi test.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas_2.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.out gas_5.in gas.out_scored.mol2 test.mol2
| |
| − | 1AAQ_yesG.mol2 gas_3.out_scored.mol2 gas_5.out no_charge test_nocharge.mol2
| |
| − | gas_2.in gas_4.in gas_5.out_scored.mol2 no_gas.in
| |
| − | gas_2.out gas_4.out gas.in no_gas.out
| |
| − | gas_3.in gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas_2.in
| |
| − | (base) [ehspector@login1 gas_teiger]$ dock6 -i gas_2.in -o gas_2.out
| |
| − | (base) [ehspector@login1 gas_teiger]$ vi gas_2.out_scored.mol2
| |
| − | (base) [ehspector@login1 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@login1 4s0v]$ cd ../../
| |
| − | (base) [ehspector@login1 rizzo]$ home
| |
| − | (base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
| |
| − | accessories/ dock/ gbsa_grids/ mopac6/ resp/
| |
| − | antechamber/ docktools/ grid/ rdkit/ tleap/
| |
| − | (base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
| |
| − | accessories/ dock/ gbsa_grids/ mopac6/ resp/
| |
| − | antechamber/ docktools/ grid/ rdkit/ tleap/
| |
| − | (base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/
| |
| − | accessories/ dock/ gbsa_grids/ mopac6/ resp/
| |
| − | antechamber/ docktools/ grid/ rdkit/ tleap/
| |
| − | (base) [ehspector@login1 espector]$ cd builds/alpha_branch/src/dock
| |
| − | (base) [ehspector@login1 dock]$ vi dockmol.cpp
| |
| − | \(base) [ehspector@login1 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@login1 dock]$ vi library_file.cpp
| |
| − | (base) [ehspector@login1 dock]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP 5EEN % ls
| |
| − | 5een.lig.min_scored.mol2 5een_noH_nocH.mol2
| |
| − | 5een.pdb 5een_protein_only.pdb
| |
| − | 5een.sph 5een_surface.dms
| |
| − | 5een_H_cH.mol2 fad_scored.mol2
| |
| − | 5een_ligand_H_cH.mol2 flex_scored.mol2
| |
| − | 5een_ligand_noH_nocH.mol2 rigid_scored.mol2
| |
| − | 5een_ligand_only.pdb selected_spheres.sph
| |
| − | (base) supremestudier@Evans-MBP 5EEN % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ ls
| |
| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@milan2 ~]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/
| |
| − | (base) [ehspector@milan2 1O86]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan2 1O86]$ cd 005_dock/
| |
| − | (base) [ehspector@milan2 005_dock]$ cd rigid/
| |
| − | (base) [ehspector@milan2 rigid]$ ls
| |
| − | rigid_conformers.mol2 rigid.in rigid.out rigid_scored.mol2 rigid.sh
| |
| − | (base) [ehspector@milan2 rigid]$ cd ..
| |
| − | (base) [ehspector@milan2 005_dock]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 5EEN/005_dock/flex/
| |
| − | (base) [ehspector@milan2 flex]$ vi flex.out
| |
| − | (base) [ehspector@milan2 flex]$ vi flex.in
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ rm flex.out
| |
| − | (base) [ehspector@milan2 flex]$ bash flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ vi flex.out
| |
| − | (base) [ehspector@milan2 flex]$ grep -c "Name" flex_scored.mol2
| |
| − | 46
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ vi flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ ls
| |
| − | flex_conformers.mol2 flex.in flex_orients.mol2 flex.out flex_scored.mol2 flex.sh
| |
| − | (base) [ehspector@milan2 flex]$ which dock6
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/bin/dock6
| |
| − | (base) [ehspector@milan2 flex]$ vi ~/.bashrc
| |
| − | (base) [ehspector@milan2 flex]$ cd ..
| |
| − | (base) [ehspector@milan2 005_dock]$ cd ..
| |
| − | (base) [ehspector@milan2 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan2 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_cartesian_min Notes.txt
| |
| − | 002_surface_spheres 005_dock 008_rescore Robs_2w26
| |
| − | 003_gridbox 006_virtual_screening commands.txt test4.tar
| |
| − | (base) [ehspector@milan2 2w26]$ cd 004_energymin/
| |
| − | (base) [ehspector@milan2 004_energymin]$ ls
| |
| − | 2w26.lig.min_scored.mol2 min.in min.out min.sh
| |
| − | (base) [ehspector@milan2 004_energymin]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_cartesian_min Notes.txt
| |
| − | 002_surface_spheres 005_dock 008_rescore Robs_2w26
| |
| − | 003_gridbox 006_virtual_screening commands.txt test4.tar
| |
| − | (base) [ehspector@milan2 2w26]$ mv 006_virtual_screening/ 006_footprint
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_cartesian_min Notes.txt
| |
| − | 002_surface_spheres 005_dock 008_rescore Robs_2w26
| |
| − | 003_gridbox 006_footprint commands.txt test4.tar
| |
| − | (base) [ehspector@milan2 2w26]$ cd 006_footprint/
| |
| − | (base) [ehspector@milan2 006_footprint]$ touch footprint.in
| |
| − | (base) [ehspector@milan2 006_footprint]$ ls
| |
| − | footprint.in
| |
| − | (base) [ehspector@milan2 006_footprint]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cp 003_gridbox/grid.sh 006_footprint/foot.sh
| |
| − | (base) [ehspector@milan2 2w26]$ cd 006_footprint/
| |
| − | (base) [ehspector@milan2 006_footprint]$ vi foot.sh
| |
| − | (base) [ehspector@milan2 006_footprint]$ vi foot.sh
| |
| − | (base) [ehspector@milan2 006_footprint]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd class_project/
| |
| − | (base) [ehspector@milan2 class_project]$ ls
| |
| − | (base) [ehspector@milan2 class_project]$ ls
| |
| − | (base) [ehspector@milan2 class_project]$ cd ..
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_cartesian_min Notes.txt
| |
| − | 002_surface_spheres 005_dock 008_rescore Robs_2w26
| |
| − | 003_gridbox 006_footprint commands.txt test4.tar
| |
| − | (base) [ehspector@milan2 2w26]$ mv Notes.txt ../../
| |
| − | (base) [ehspector@milan2 2w26]$ mv commands.txt ../../
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_cartesian_min Robs_2w26
| |
| − | 002_surface_spheres 004_energymin 006_footprint 008_rescore test4.tar
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ vi Notes.txt
| |
| − | (base) [ehspector@milan2 AMS_536]$ vi commands.txt
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_cartesian_min Robs_2w26
| |
| − | 002_surface_spheres 004_energymin 006_footprint 008_rescore test4.tar
| |
| − | (base) [ehspector@milan2 2w26]$ mkdir 007_virtual_screen
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_cartesian_min Robs_2w26
| |
| − | 002_surface_spheres 005_dock 007_virtual_screen test4.tar
| |
| − | 003_gridbox 006_footprint 008_rescore
| |
| − | (base) [ehspector@milan2 2w26]$ mv 007_cartesian_min/ 008_cartesian_min
| |
| − | (base) [ehspector@milan2 2w26]$ mv 008_rescore/ 009_rescore
| |
| − | (base) [ehspector@milan2 2w26]$ cd ../5EEN/
| |
| − | (base) [ehspector@milan2 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan2 5EEN]$ mv 006_virtual_screen_mpi/ 006_footprint
| |
| − | (base) [ehspector@milan2 5EEN]$ mkdir 007_virtualscreen
| |
| − | (base) [ehspector@milan2 5EEN]$ mv 007_cartesian_min/ 008_cartesian_min
| |
| − | (base) [ehspector@milan2 5EEN]$ mv 008_rescore/ 009_rescore
| |
| − | (base) [ehspector@milan2 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore
| |
| − | 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min commands.txt
| |
| − | (base) [ehspector@milan2 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86
| |
| − | (base) [ehspector@milan2 1O86]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_cartesian_min commands.txt
| |
| − | 002_surface_spheres 004_energymin 006_virtual_screen_mpi 008_rescore
| |
| − | (base) [ehspector@milan2 1O86]$ mv 006_virtual_screen_mpi/ 006_footprint
| |
| − | (base) [ehspector@milan2 1O86]$ mkdir 007_virtualscreen
| |
| − | (base) [ehspector@milan2 1O86]$ mv 007_cartesian_min/ 008_cartesian_min
| |
| − | (base) [ehspector@milan2 1O86]$ mv 008_rescore/ 009_rescore
| |
| − | (base) [ehspector@milan2 1O86]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore
| |
| − | 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min commands.txt
| |
| − | (base) [ehspector@milan2 1O86]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ vi commands.txt
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ bash commands.txt
| |
| − | commands.txt: line 2: protein_name: Is a directory
| |
| − | commands.txt: line 3: protein_name: Is a directory
| |
| − | commands.txt: line 4: protein_name: Is a directory
| |
| − | commands.txt: line 5: protein_name: Is a directory
| |
| − | commands.txt: line 6: protein_name: Is a directory
| |
| − | commands.txt: line 10: protein_name: Is a directory
| |
| − | commands.txt: line 11: protein_name: Is a directory
| |
| − | commands.txt: line 12: protein_name: Is a directory
| |
| − | commands.txt: line 13: protein_name: Is a directory
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | 005_dock commands.txt flex protein_name Tutorials
| |
| − | class_project fixed_anchor Notes.txt rigid
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd protein_name/
| |
| − | (base) [ehspector@milan2 protein_name]$ ls
| |
| − | (base) [ehspector@milan2 protein_name]$ cd ..
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm protein_name/
| |
| − | rm: cannot remove 'protein_name/': Is a directory
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r protein_name/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm 005_dock
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r flex/
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt rigid Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r rigid/
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan2 AMS_536]$ vi commands.txt
| |
| − | (base) [ehspector@milan2 AMS_536]$ bash commands.txt
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | 001_structure 005_dock 009_rescore flex Tutorials
| |
| − | 002_surface_spheres 006_footprint class_project Notes.txt
| |
| − | 003_gridbox 007_virtualscreen commands.txt protein_name
| |
| − | 004_energymin 008_cartesian_min fixed_anchor rigid
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 001_structure/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 003_surface_spheres/
| |
| − | rm: cannot remove '003_surface_spheres/': No such file or directory
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 003_gridbox/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 004_energymin/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 005_dock/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 006_footprint/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 007_virtualscreen/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 008_cartesian_min/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 009_rescore/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r protein_name/
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt fixed_anchor flex Notes.txt rigid Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r flex
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r rigid/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r rigid/
| |
| − | rm: cannot remove 'rigid/': No such file or directory
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r flex
| |
| − | rm: cannot remove 'flex': No such file or directory
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ vi commands.txt
| |
| − | (base) [ehspector@milan2 AMS_536]$ bash commands.txt
| |
| − | mkdir: cannot create directory ‘protein_name’: File exists
| |
| − | mkdir: cannot create directory ‘protein_name’: File exists
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | 001_structure 005_dock 009_rescore flex Tutorials
| |
| − | 002_surface_spheres 006_footprint class_project Notes.txt
| |
| − | 003_gridbox 007_virtualscreen commands.txt protein_name
| |
| − | 004_energymin 008_cartesian_min fixed_anchor rigid
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r flex
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r fixed_anchor/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r rigid/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 001_structure/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 002_surface_spheres/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 003_gridbox/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 004_energymin/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 005_dock/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 006_footprint/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 007_virtualscreen/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 008_cartesian_min/
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r 009_rescore/
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt protein_name Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd protein_name/
| |
| − | (base) [ehspector@milan2 protein_name]$ ls
| |
| − | (base) [ehspector@milan2 protein_name]$ cd ..
| |
| − | (base) [ehspector@milan2 AMS_536]$ sinfo
| |
| − | PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
| |
| − | a100 up 8:00:00 1 mix@ a100-02
| |
| − | a100 up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100 up 8:00:00 1 drain* a100-01
| |
| − | a100 up 8:00:00 4 mix a100-[03-05,11]
| |
| − | a100 up 8:00:00 3 alloc a100-[06,08,10]
| |
| − | a100-large up 8:00:00 1 mix@ a100-02
| |
| − | a100-large up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-large up 8:00:00 1 drain* a100-01
| |
| − | a100-large up 8:00:00 4 mix a100-[03-05,11]
| |
| − | a100-large up 8:00:00 3 alloc a100-[06,08,10]
| |
| − | a100-long up 2-00:00:00 1 mix@ a100-02
| |
| − | a100-long up 2-00:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-long up 2-00:00:00 1 drain* a100-01
| |
| − | a100-long up 2-00:00:00 4 mix a100-[03-05,11]
| |
| − | a100-long up 2-00:00:00 3 alloc a100-[06,08,10]
| |
| − | debug-40core up 1:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | debug-40core up 1:00:00 2 drain* dn[031,037]
| |
| − | debug-40core up 1:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | debug-40core up 1:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | extended-40core up 7-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | extended-40core up 7-00:00:00 2 drain* dn[031,037]
| |
| − | extended-40core up 7-00:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | extended-40core up 7-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | extended-40core-shared up 3-12:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | extended-40core-shared up 3-12:00:00 2 drain* dn[031,037]
| |
| − | extended-40core-shared up 3-12:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | extended-40core-shared up 3-12:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | extended-96core up 7-00:00:00 1 mix@ dg040
| |
| − | extended-96core up 7-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | extended-96core up 7-00:00:00 1 mix dg023
| |
| − | extended-96core up 7-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | extended-96core-shared up 3-12:00:00 1 mix@ dg040
| |
| − | extended-96core-shared up 3-12:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | extended-96core-shared up 3-12:00:00 1 mix dg023
| |
| − | extended-96core-shared up 3-12:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 alloc@ xm048
| |
| − | hbm-1tb-long-96core up 2-00:00:00 2 alloc xm[045,047]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 idle xm046
| |
| − | hbm-extended-96core up 7-00:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
| |
| − | hbm-extended-96core up 7-00:00:00 1 drain xm017
| |
| − | hbm-extended-96core up 7-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-large-96core up 8:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
| |
| − | hbm-large-96core up 8:00:00 1 drain xm017
| |
| − | hbm-large-96core up 8:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-long-96core up 2-00:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
| |
| − | hbm-long-96core up 2-00:00:00 1 drain xm017
| |
| − | hbm-long-96core up 2-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-medium-96core up 12:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
| |
| − | hbm-medium-96core up 12:00:00 1 drain xm017
| |
| − | hbm-medium-96core up 12:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-short-96core up 4:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
| |
| − | hbm-short-96core up 4:00:00 1 drain xm017
| |
| − | hbm-short-96core up 4:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
| |
| − | large-40core up 8:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | large-40core up 8:00:00 2 drain* dn[031,037]
| |
| − | large-40core up 8:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | large-40core up 8:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | large-96core up 8:00:00 1 mix@ dg040
| |
| − | large-96core up 8:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | large-96core up 8:00:00 1 mix dg023
| |
| − | large-96core up 8:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | long-40core up 2-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | long-40core up 2-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core up 2-00:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | long-40core up 2-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | long-40core-shared up 1-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | long-40core-shared up 1-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core-shared up 1-00:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | long-40core-shared up 1-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | long-96core up 2-00:00:00 1 mix@ dg040
| |
| − | long-96core up 2-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | long-96core up 2-00:00:00 1 mix dg023
| |
| − | long-96core up 2-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | long-96core-shared up 1-00:00:00 1 mix@ dg040
| |
| − | long-96core-shared up 1-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | long-96core-shared up 1-00:00:00 1 mix dg023
| |
| − | long-96core-shared up 1-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | medium-40core up 12:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | medium-40core up 12:00:00 2 drain* dn[031,037]
| |
| − | medium-40core up 12:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | medium-40core up 12:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | medium-96core up 12:00:00 1 mix@ dg040
| |
| − | medium-96core up 12:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | medium-96core up 12:00:00 1 mix dg023
| |
| − | medium-96core up 12:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | ood-short-96core up 4:00:00 1 idle dg038
| |
| − | rn-long-40core up 8-08:00:00 12 idle rn[001-012]
| |
| − | short-40core up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | short-40core up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core up 4:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | short-40core up 4:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | short-40core-shared up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | short-40core-shared up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core-shared up 4:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | short-40core-shared up 4:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | short-96core up 4:00:00 1 mix@ dg040
| |
| − | short-96core up 4:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | short-96core up 4:00:00 1 mix dg023
| |
| − | short-96core up 4:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | short-96core-shared up 4:00:00 1 mix@ dg040
| |
| − | short-96core-shared up 4:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | short-96core-shared up 4:00:00 1 mix dg023
| |
| − | short-96core-shared up 4:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt protein_name Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ rm -r protein_name
| |
| − | (base) [ehspector@milan2 AMS_536]$ vi ~/.bashrc
| |
| − | (base) [ehspector@milan2 AMS_536]$ source ~/.bashrc
| |
| − | (base) [ehspector@milan2 AMS_536]$ avail
| |
| − | PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
| |
| − | a100 up 8:00:00 1 mix@ a100-02
| |
| − | a100 up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100 up 8:00:00 1 drain* a100-01
| |
| − | a100 up 8:00:00 4 mix a100-[03-05,11]
| |
| − | a100 up 8:00:00 3 alloc a100-[06,08,10]
| |
| − | a100-large up 8:00:00 1 mix@ a100-02
| |
| − | a100-large up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-large up 8:00:00 1 drain* a100-01
| |
| − | a100-large up 8:00:00 4 mix a100-[03-05,11]
| |
| − | a100-large up 8:00:00 3 alloc a100-[06,08,10]
| |
| − | a100-long up 2-00:00:00 1 mix@ a100-02
| |
| − | a100-long up 2-00:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-long up 2-00:00:00 1 drain* a100-01
| |
| − | a100-long up 2-00:00:00 4 mix a100-[03-05,11]
| |
| − | a100-long up 2-00:00:00 3 alloc a100-[06,08,10]
| |
| − | debug-40core up 1:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | debug-40core up 1:00:00 2 drain* dn[031,037]
| |
| − | debug-40core up 1:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | debug-40core up 1:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | extended-40core up 7-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | extended-40core up 7-00:00:00 2 drain* dn[031,037]
| |
| − | extended-40core up 7-00:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | extended-40core up 7-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | extended-40core-shared up 3-12:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | extended-40core-shared up 3-12:00:00 2 drain* dn[031,037]
| |
| − | extended-40core-shared up 3-12:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | extended-40core-shared up 3-12:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | extended-96core up 7-00:00:00 1 mix@ dg040
| |
| − | extended-96core up 7-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | extended-96core up 7-00:00:00 1 mix dg023
| |
| − | extended-96core up 7-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | extended-96core-shared up 3-12:00:00 1 mix@ dg040
| |
| − | extended-96core-shared up 3-12:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | extended-96core-shared up 3-12:00:00 1 mix dg023
| |
| − | extended-96core-shared up 3-12:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 alloc@ xm048
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 alloc xm047
| |
| − | hbm-1tb-long-96core up 2-00:00:00 2 idle xm[045-046]
| |
| − | hbm-extended-96core up 7-00:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
| |
| − | hbm-extended-96core up 7-00:00:00 1 drain xm017
| |
| − | hbm-extended-96core up 7-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-large-96core up 8:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
| |
| − | hbm-large-96core up 8:00:00 1 drain xm017
| |
| − | hbm-large-96core up 8:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-long-96core up 2-00:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
| |
| − | hbm-long-96core up 2-00:00:00 1 drain xm017
| |
| − | hbm-long-96core up 2-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-medium-96core up 12:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
| |
| − | hbm-medium-96core up 12:00:00 1 drain xm017
| |
| − | hbm-medium-96core up 12:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-short-96core up 4:00:00 15 alloc@ xm[002,004-005,008,013,015,025,027-028,032,039,041,044,049,051]
| |
| − | hbm-short-96core up 4:00:00 1 drain xm017
| |
| − | hbm-short-96core up 4:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,029-031,033-038,040,042-043,050,052-094]
| |
| − | large-40core up 8:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | large-40core up 8:00:00 2 drain* dn[031,037]
| |
| − | large-40core up 8:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | large-40core up 8:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | large-96core up 8:00:00 1 mix@ dg040
| |
| − | large-96core up 8:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | large-96core up 8:00:00 1 mix dg023
| |
| − | large-96core up 8:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | long-40core up 2-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | long-40core up 2-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core up 2-00:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | long-40core up 2-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | long-40core-shared up 1-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | long-40core-shared up 1-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core-shared up 1-00:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | long-40core-shared up 1-00:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | long-96core up 2-00:00:00 1 mix@ dg040
| |
| − | long-96core up 2-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | long-96core up 2-00:00:00 1 mix dg023
| |
| − | long-96core up 2-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | long-96core-shared up 1-00:00:00 1 mix@ dg040
| |
| − | long-96core-shared up 1-00:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | long-96core-shared up 1-00:00:00 1 mix dg023
| |
| − | long-96core-shared up 1-00:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | medium-40core up 12:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | medium-40core up 12:00:00 2 drain* dn[031,037]
| |
| − | medium-40core up 12:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | medium-40core up 12:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | medium-96core up 12:00:00 1 mix@ dg040
| |
| − | medium-96core up 12:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | medium-96core up 12:00:00 1 mix dg023
| |
| − | medium-96core up 12:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | ood-short-96core up 4:00:00 1 idle dg038
| |
| − | rn-long-40core up 8-08:00:00 12 idle rn[001-012]
| |
| − | short-40core up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | short-40core up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core up 4:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | short-40core up 4:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | short-40core-shared up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | short-40core-shared up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core-shared up 4:00:00 9 mix dn[001,003-005,007,018,027,051,060]
| |
| − | short-40core-shared up 4:00:00 44 alloc dn[002,006,008,010-017,019-025,028,030,032,034,036,039-044,046-050,052-059,061-062]
| |
| − | short-96core up 4:00:00 1 mix@ dg040
| |
| − | short-96core up 4:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | short-96core up 4:00:00 1 mix dg023
| |
| − | short-96core up 4:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | short-96core-shared up 4:00:00 1 mix@ dg040
| |
| − | short-96core-shared up 4:00:00 21 alloc@ dg[006,008-011,013,015,019,024,027-029,033-034,037,039,041,043-044,046,048]
| |
| − | short-96core-shared up 4:00:00 1 mix dg023
| |
| − | short-96core-shared up 4:00:00 24 alloc dg[001-005,007,012,014,016-018,020-022,025-026,030-032,035-036,042,045,047]
| |
| − | (base) [ehspector@milan2 AMS_536]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | (base) [ehspector@milan2 AMS_536]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP 5EEN % ls
| |
| − | 5een.lig.min_scored.mol2 5een_noH_nocH.mol2
| |
| − | 5een.pdb 5een_protein_only.pdb
| |
| − | 5een.sph 5een_surface.dms
| |
| − | 5een_H_cH.mol2 fad_scored.mol2
| |
| − | 5een_ligand_H_cH.mol2 flex_scored.mol2
| |
| − | 5een_ligand_noH_nocH.mol2 rigid_scored.mol2
| |
| − | 5een_ligand_only.pdb selected_spheres.sph
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ home
| |
| − | (base) [ehspector@milan1 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@milan1 espector]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/006_footprint/
| |
| − | (base) [ehspector@milan1 006_footprint]$ ls
| |
| − | footprint.in foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi footprint.in
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd
| |
| − | (base) [ehspector@milan1 ~]$ cd ../../
| |
| − | (base) [ehspector@milan1 gpfs]$ cd projects/AMS536/2025/transfers/
| |
| − | (base) [ehspector@milan1 transfers]$ ls
| |
| − | 2025_02_12a_test.tar
| |
| − | (base) [ehspector@milan1 transfers]$ cd ..
| |
| − | (base) [ehspector@milan1 2025]$ ls
| |
| − | 1EVE_DOCK_VS additional_files INSPH robbashrc_file rotations transfers
| |
| − | (base) [ehspector@milan1 2025]$ cd transfers/
| |
| − | (base) [ehspector@milan1 transfers]$ pwd
| |
| − | /gpfs/projects/AMS536/2025/transfers
| |
| − | (base) [ehspector@milan1 transfers]$ ^C
| |
| − | (base) [ehspector@milan1 transfers]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp /gpfs/projects/AMS536/2025/transfers/2025_02_12a_test.tar .
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2025_02_12a_test.tar 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ mv 2025_02_12a_test.tar 2w26/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_virtual_screen 009_rescore Robs_2w26
| |
| − | 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min 2025_02_12a_test.tar test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ tar -xf 2025_02_12a_test.tar
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min 2W26
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ mv 2W26/ Robs_new_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_new_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ ls
| |
| − | 000_test 001_structure 002_spheres 003_grid 004_dock 005_analysis 006_ga_lib 007_ga_run1
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/
| |
| − | (base) [ehspector@milan1 005_analysis]$ ls
| |
| − | 01fps_footprint_scored.txt 01fps_hbond_scored.txt 01fps.log1 01fps.out 01fps.sh
| |
| − | 01fps_footprint_scored.txt.pdf 01fps.in 01fps.log2 01fps_scored.mol2
| |
| − | (base) [ehspector@milan1 005_analysis]$ cd ..
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/005_analysis/01fps.in 006_footprint/footprint.in
| |
| − | (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/005_analysis/
| |
| − | (base) [ehspector@milan1 005_analysis]$ vi 01fps
| |
| − | (base) [ehspector@milan1 005_analysis]$ vi 01fps.sh
| |
| − | (base) [ehspector@milan1 005_analysis]$ vi 01fps.sh
| |
| − | (base) [ehspector@milan1 005_analysis]$ vi 01fps.sh
| |
| − | (base) [ehspector@milan1 005_analysis]$ cd ../../006_footprint/
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi footprint.in
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi footprint.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ ls
| |
| − | footprint.in foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi footprint.in
| |
| − | (base) [ehspector@milan1 006_footprint]$ cd ../001_structure/
| |
| − | (base) [ehspector@milan1 001_structure]$ ls
| |
| − | 2w26_ligand_H_cH.mol2 2w26_ligand_noH_nocH.mol2 2w26_protein_H_cH.mol2 2w26_protein_noH_nocH.mol2
| |
| − | (base) [ehspector@milan1 001_structure]$ cd ../006_footprint/
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi footprint.in
| |
| − | (base) [ehspector@milan1 006_footprint]$ bash foot.sh
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type rigid
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy no
| |
| − |
| |
| − | Molecule Library Input Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_atom_file ../004_energymin/2w26.lig.min_scored.mol2
| |
| − | limit_max_ligands no
| |
| − | skip_molecule no
| |
| − | read_mol_solvation no
| |
| − | calculate_rmsd no
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter no
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand no
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter no
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules yes
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary no
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary no
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | gist_score_primary no
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | multigrid_score_primary no
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | dock3.5_score_primary no
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | continuous_score_primary no
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | footprint_similarity_score_primary yes
| |
| − | fps_score_use_footprint_reference_mol2 yes
| |
| − | fps_score_footprint_reference_mol2_filename ../001_structure/2w26_ligand_H_cH.mol2
| |
| − | fps_score_foot_compare_type Euclidean
| |
| − | -------------------------------------------------------------
| |
| − | You chose to use the Euclidean distance as the metric
| |
| − | to compare the footprints. When the value is 0 then
| |
| − | there is perfect agreement between the two footprints.
| |
| − | As the agreement gets worse between the two
| |
| − | footprints the value increases.
| |
| − | -------------------------------------------------------------
| |
| − | fps_score_normalize_foot no
| |
| − | fps_score_foot_comp_all_residue yes
| |
| − | fps_score_receptor_filename ../001_structure/2w26_protein_H_cH.mol2
| |
| − | fps_score_vdw_att_exp 6
| |
| − | fps_score_vdw_rep_exp 9
| |
| − | fps_score_vdw_rep_rad_scale 1
| |
| − | fps_score_use_distance_dependent_dielectric yes
| |
| − | fps_score_dielectric 4.0
| |
| − | fps_score_vdw_fp_scale 1
| |
| − | fps_score_es_fp_scale 1
| |
| − | fps_score_hb_fp_scale 0
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand no
| |
| − | simplex_final_min no
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model all
| |
| − | vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
| |
| − | flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
| |
| − | flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
| |
| − |
| |
| − | Molecule Library Output Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_outfile_prefix footprint
| |
| − | write_mol_solvation no
| |
| − | write_footprints yes
| |
| − | write_hbonds yes
| |
| − | write_orientations no
| |
| − | num_scored_conformers 1
| |
| − | score_threshold 100.0
| |
| − | rank_ligands no
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | Initializing Library File Routines...
| |
| − |
| |
| − | To cite Footprint Similarity Score use:
| |
| − | Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
| |
| − |
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − |
| |
| − | -----------------------------------
| |
| − | Molecule: 2w26.pdb
| |
| − |
| |
| − | Elapsed time for docking: 0.008 seconds
| |
| − |
| |
| − | Anchors: 1
| |
| − | Orientations: 1
| |
| − | Conformations: 1
| |
| − |
| |
| − | Footprint_Similarity_Score: 0.761241
| |
| − | FPS_vdw_energy: -76.920898
| |
| − | FPS_es_energy: -2.930423
| |
| − | FPS_vdw+es_energy: -79.851318
| |
| − | FPS_num_hbond: 2
| |
| − | FPS_vdw_fps: 0.642335
| |
| − | FPS_es_fps: 0.118906
| |
| − | FPS_hb_fps: 0.000000
| |
| − | FPS_vdw_fp_numres: 286
| |
| − | FPS_es_fp_numres: 286
| |
| − | FPS_hb_fp_numres: 286
| |
| − |
| |
| − |
| |
| − | 1 Molecules Processed
| |
| − | Total elapsed time: 0.587 seconds
| |
| − | Number of molecules per second: 1.705
| |
| − | Virtual memory used for this process: 80220 kilobytes
| |
| − | Physical memory used for this process: 8192 kilobytes
| |
| − | Traceback (most recent call last):
| |
| − | File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 9, in <module>
| |
| − | import matplotlib
| |
| − | ModuleNotFoundError: No module named 'matplotlib'
| |
| − | (base) [ehspector@milan1 006_footprint]$ module load python
| |
| − | (base) [ehspector@milan1 006_footprint]$ module list
| |
| − | Currently Loaded Modulefiles:
| |
| − | 1) slurm/seawulf3/21.08.8 3) gcc/13.2.0 5) gcc-stack
| |
| − | 2) shared 4) mvapich2/gcc13.2/2.3.7 6) python/3.11.2
| |
| − | (base) [ehspector@milan1 006_footprint]$ bash foot.sh
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type rigid
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy no
| |
| − |
| |
| − | Molecule Library Input Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_atom_file ../004_energymin/2w26.lig.min_scored.mol2
| |
| − | limit_max_ligands no
| |
| − | skip_molecule no
| |
| − | read_mol_solvation no
| |
| − | calculate_rmsd no
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter no
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand no
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter no
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules yes
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary no
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary no
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | gist_score_primary no
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | multigrid_score_primary no
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | dock3.5_score_primary no
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | continuous_score_primary no
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | footprint_similarity_score_primary yes
| |
| − | fps_score_use_footprint_reference_mol2 yes
| |
| − | fps_score_footprint_reference_mol2_filename ../001_structure/2w26_ligand_H_cH.mol2
| |
| − | fps_score_foot_compare_type Euclidean
| |
| − | -------------------------------------------------------------
| |
| − | You chose to use the Euclidean distance as the metric
| |
| − | to compare the footprints. When the value is 0 then
| |
| − | there is perfect agreement between the two footprints.
| |
| − | As the agreement gets worse between the two
| |
| − | footprints the value increases.
| |
| − | -------------------------------------------------------------
| |
| − | fps_score_normalize_foot no
| |
| − | fps_score_foot_comp_all_residue yes
| |
| − | fps_score_receptor_filename ../001_structure/2w26_protein_H_cH.mol2
| |
| − | fps_score_vdw_att_exp 6
| |
| − | fps_score_vdw_rep_exp 9
| |
| − | fps_score_vdw_rep_rad_scale 1
| |
| − | fps_score_use_distance_dependent_dielectric yes
| |
| − | fps_score_dielectric 4.0
| |
| − | fps_score_vdw_fp_scale 1
| |
| − | fps_score_es_fp_scale 1
| |
| − | fps_score_hb_fp_scale 0
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand no
| |
| − | simplex_final_min no
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model all
| |
| − | vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
| |
| − | flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
| |
| − | flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
| |
| − |
| |
| − | Molecule Library Output Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_outfile_prefix footprint
| |
| − | write_mol_solvation no
| |
| − | write_footprints yes
| |
| − | write_hbonds yes
| |
| − | write_orientations no
| |
| − | num_scored_conformers 1
| |
| − | score_threshold 100.0
| |
| − | rank_ligands no
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | Initializing Library File Routines...
| |
| − |
| |
| − | To cite Footprint Similarity Score use:
| |
| − | Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
| |
| − |
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − |
| |
| − | -----------------------------------
| |
| − | Molecule: 2w26.pdb
| |
| − |
| |
| − | Elapsed time for docking: 0.008 seconds
| |
| − |
| |
| − | Anchors: 1
| |
| − | Orientations: 1
| |
| − | Conformations: 1
| |
| − |
| |
| − | Footprint_Similarity_Score: 0.761241
| |
| − | FPS_vdw_energy: -76.920898
| |
| − | FPS_es_energy: -2.930423
| |
| − | FPS_vdw+es_energy: -79.851318
| |
| − | FPS_num_hbond: 2
| |
| − | FPS_vdw_fps: 0.642335
| |
| − | FPS_es_fps: 0.118906
| |
| − | FPS_hb_fps: 0.000000
| |
| − | FPS_vdw_fp_numres: 286
| |
| − | FPS_es_fp_numres: 286
| |
| − | FPS_hb_fp_numres: 286
| |
| − |
| |
| − |
| |
| − | 1 Molecules Processed
| |
| − | Total elapsed time: 0.487 seconds
| |
| − | Number of molecules per second: 2.053
| |
| − | Virtual memory used for this process: 80224 kilobytes
| |
| − | Physical memory used for this process: 8192 kilobytes
| |
| − | Traceback (most recent call last):
| |
| − | File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
| |
| − | main()
| |
| − | File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
| |
| − | (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
| |
| − | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| |
| − | File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 20, in identify_residues
| |
| − | fp_file = open(filename,'r')
| |
| − | ^^^^^^^^^^^^^^^^^^
| |
| − | FileNotFoundError: [Errno 2] No such file or directory: '2w26_footprint.out_footprint_scored.txt'
| |
| − | (base) [ehspector@milan1 006_footprint]$ ls
| |
| − | footprint_footprint_scored.txt footprint_hbond_scored.txt footprint.in footprint_scored.mol2 foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi footprint.in
| |
| − | (base) [ehspector@milan1 006_footprint]$ bash foot.sh
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type rigid
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy no
| |
| − |
| |
| − | Molecule Library Input Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_atom_file ../004_energymin/2w26.lig.min_scored.mol2
| |
| − | limit_max_ligands no
| |
| − | skip_molecule no
| |
| − | read_mol_solvation no
| |
| − | calculate_rmsd no
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter no
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand no
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter no
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules yes
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary no
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary no
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | gist_score_primary no
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | multigrid_score_primary no
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | dock3.5_score_primary no
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | continuous_score_primary no
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | footprint_similarity_score_primary yes
| |
| − | fps_score_use_footprint_reference_mol2 yes
| |
| − | fps_score_footprint_reference_mol2_filename ../001_structure/2w26_ligand_H_cH.mol2
| |
| − | fps_score_foot_compare_type Euclidean
| |
| − | -------------------------------------------------------------
| |
| − | You chose to use the Euclidean distance as the metric
| |
| − | to compare the footprints. When the value is 0 then
| |
| − | there is perfect agreement between the two footprints.
| |
| − | As the agreement gets worse between the two
| |
| − | footprints the value increases.
| |
| − | -------------------------------------------------------------
| |
| − | fps_score_normalize_foot no
| |
| − | fps_score_foot_comp_all_residue yes
| |
| − | fps_score_receptor_filename ../001_structure/2w26_protein_H_cH.mol2
| |
| − | fps_score_vdw_att_exp 6
| |
| − | fps_score_vdw_rep_exp 9
| |
| − | fps_score_vdw_rep_rad_scale 1
| |
| − | fps_score_use_distance_dependent_dielectric yes
| |
| − | fps_score_dielectric 4.0
| |
| − | fps_score_vdw_fp_scale 1
| |
| − | fps_score_es_fp_scale 1
| |
| − | fps_score_hb_fp_scale 0
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand no
| |
| − | simplex_final_min no
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model all
| |
| − | vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
| |
| − | flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
| |
| − | flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
| |
| − |
| |
| − | Molecule Library Output Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_outfile_prefix 2w26
| |
| − | write_mol_solvation no
| |
| − | write_footprints yes
| |
| − | write_hbonds yes
| |
| − | write_orientations no
| |
| − | num_scored_conformers 1
| |
| − | score_threshold 100.0
| |
| − | rank_ligands no
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | Initializing Library File Routines...
| |
| − |
| |
| − | To cite Footprint Similarity Score use:
| |
| − | Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
| |
| − |
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − |
| |
| − | -----------------------------------
| |
| − | Molecule: 2w26.pdb
| |
| − |
| |
| − | Elapsed time for docking: 0.008 seconds
| |
| − |
| |
| − | Anchors: 1
| |
| − | Orientations: 1
| |
| − | Conformations: 1
| |
| − |
| |
| − | Footprint_Similarity_Score: 0.761241
| |
| − | FPS_vdw_energy: -76.920898
| |
| − | FPS_es_energy: -2.930423
| |
| − | FPS_vdw+es_energy: -79.851318
| |
| − | FPS_num_hbond: 2
| |
| − | FPS_vdw_fps: 0.642335
| |
| − | FPS_es_fps: 0.118906
| |
| − | FPS_hb_fps: 0.000000
| |
| − | FPS_vdw_fp_numres: 286
| |
| − | FPS_es_fp_numres: 286
| |
| − | FPS_hb_fp_numres: 286
| |
| − |
| |
| − |
| |
| − | 1 Molecules Processed
| |
| − | Total elapsed time: 0.525 seconds
| |
| − | Number of molecules per second: 1.905
| |
| − | Virtual memory used for this process: 80224 kilobytes
| |
| − | Physical memory used for this process: 8192 kilobytes
| |
| − | Traceback (most recent call last):
| |
| − | File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
| |
| − | main()
| |
| − | File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
| |
| − | (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
| |
| − | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| |
| − | File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 20, in identify_residues
| |
| − | fp_file = open(filename,'r')
| |
| − | ^^^^^^^^^^^^^^^^^^
| |
| − | FileNotFoundError: [Errno 2] No such file or directory: '2w26_footprint.out_footprint_scored.txt'
| |
| − | (base) [ehspector@milan1 006_footprint]$ ls
| |
| − | 2w26_footprint_scored.txt footprint_footprint_scored.txt footprint_scored.mol2
| |
| − | 2w26_hbond_scored.txt footprint_hbond_scored.txt foot.sh
| |
| − | 2w26_scored.mol2 footprint.in
| |
| − | (base) [ehspector@milan1 006_footprint]$ rm *mol2
| |
| − | (base) [ehspector@milan1 006_footprint]$ ls
| |
| − | 2w26_footprint_scored.txt footprint_footprint_scored.txt footprint.in
| |
| − | 2w26_hbond_scored.txt footprint_hbond_scored.txt foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ rm *.txt
| |
| − | (base) [ehspector@milan1 006_footprint]$ bash foot.sh
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type rigid
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy no
| |
| − |
| |
| − | Molecule Library Input Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_atom_file ../004_energymin/2w26.lig.min_scored.mol2
| |
| − | limit_max_ligands no
| |
| − | skip_molecule no
| |
| − | read_mol_solvation no
| |
| − | calculate_rmsd no
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter no
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand no
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter no
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules yes
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary no
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary no
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | gist_score_primary no
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | multigrid_score_primary no
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | dock3.5_score_primary no
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | continuous_score_primary no
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | footprint_similarity_score_primary yes
| |
| − | fps_score_use_footprint_reference_mol2 yes
| |
| − | fps_score_footprint_reference_mol2_filename ../001_structure/2w26_ligand_H_cH.mol2
| |
| − | fps_score_foot_compare_type Euclidean
| |
| − | -------------------------------------------------------------
| |
| − | You chose to use the Euclidean distance as the metric
| |
| − | to compare the footprints. When the value is 0 then
| |
| − | there is perfect agreement between the two footprints.
| |
| − | As the agreement gets worse between the two
| |
| − | footprints the value increases.
| |
| − | -------------------------------------------------------------
| |
| − | fps_score_normalize_foot no
| |
| − | fps_score_foot_comp_all_residue yes
| |
| − | fps_score_receptor_filename ../001_structure/2w26_protein_H_cH.mol2
| |
| − | fps_score_vdw_att_exp 6
| |
| − | fps_score_vdw_rep_exp 9
| |
| − | fps_score_vdw_rep_rad_scale 1
| |
| − | fps_score_use_distance_dependent_dielectric yes
| |
| − | fps_score_dielectric 4.0
| |
| − | fps_score_vdw_fp_scale 1
| |
| − | fps_score_es_fp_scale 1
| |
| − | fps_score_hb_fp_scale 0
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand no
| |
| − | simplex_final_min no
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model all
| |
| − | vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
| |
| − | flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
| |
| − | flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
| |
| − |
| |
| − | Molecule Library Output Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_outfile_prefix 2w26
| |
| − | write_mol_solvation no
| |
| − | write_footprints yes
| |
| − | write_hbonds yes
| |
| − | write_orientations no
| |
| − | num_scored_conformers 1
| |
| − | score_threshold 100.0
| |
| − | rank_ligands no
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | Initializing Library File Routines...
| |
| − |
| |
| − | To cite Footprint Similarity Score use:
| |
| − | Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
| |
| − |
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Ca in Fingerprint::return_atom_type not recognized
| |
| − |
| |
| − | -----------------------------------
| |
| − | Molecule: 2w26.pdb
| |
| − |
| |
| − | Elapsed time for docking: 0.008 seconds
| |
| − |
| |
| − | Anchors: 1
| |
| − | Orientations: 1
| |
| − | Conformations: 1
| |
| − |
| |
| − | Footprint_Similarity_Score: 0.761241
| |
| − | FPS_vdw_energy: -76.920898
| |
| − | FPS_es_energy: -2.930423
| |
| − | FPS_vdw+es_energy: -79.851318
| |
| − | FPS_num_hbond: 2
| |
| − | FPS_vdw_fps: 0.642335
| |
| − | FPS_es_fps: 0.118906
| |
| − | FPS_hb_fps: 0.000000
| |
| − | FPS_vdw_fp_numres: 286
| |
| − | FPS_es_fp_numres: 286
| |
| − | FPS_hb_fp_numres: 286
| |
| − |
| |
| − |
| |
| − | 1 Molecules Processed
| |
| − | Total elapsed time: 0.585 seconds
| |
| − | Number of molecules per second: 1.710
| |
| − | Virtual memory used for this process: 80224 kilobytes
| |
| − | Physical memory used for this process: 8192 kilobytes
| |
| − | No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
| |
| − | /gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
| |
| − | plt.show()
| |
| − | (base) [ehspector@milan1 006_footprint]$ ls
| |
| − | 2w26_footprint_scored.txt 2w26_hbond_scored.txt footprint.in
| |
| − | 2w26_footprint_scored.txt.pdf 2w26_scored.mol2 foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_new_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ ls
| |
| − | 000_test 001_structure 002_spheres 003_grid 004_dock 005_analysis 006_ga_lib 007_ga_run1
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/
| |
| − | (base) [ehspector@milan1 005_analysis]$ ls
| |
| − | 01fps_footprint_scored.txt 01fps_hbond_scored.txt 01fps.log1 01fps.out 01fps.sh
| |
| − | 01fps_footprint_scored.txt.pdf 01fps.in 01fps.log2 01fps_scored.mol2
| |
| − | (base) [ehspector@milan1 005_analysis]$ cd ../006_ga_lib/
| |
| − | (base) [ehspector@milan1 006_ga_lib]$ ls
| |
| − | 01lib.sh 2W26.fraglib.out 2W26_fragout_scored.mol2
| |
| − | 02combine.sh 2W26_fraglib_rigid.mol2 full_fraglib.dat
| |
| − | 2W26.fraglib.in 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat
| |
| − | 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 unique_full_sorted_fraglib.dat
| |
| − | 2W26.fraglib.log 2W26_fraglib_torenv.dat
| |
| − | (base) [ehspector@milan1 006_ga_lib]$ cd ..
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_new_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ ls
| |
| − | 000_test 001_structure 002_spheres 003_grid 004_dock 005_analysis 006_ga_lib 007_ga_run1
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd 000_test/
| |
| − | (base) [ehspector@milan1 000_test]$ ls
| |
| − | test_dock.in
| |
| − | (base) [ehspector@milan1 000_test]$ cd ..
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd 004_dock/
| |
| − | (base) [ehspector@milan1 004_dock]$ ls
| |
| − | 01min.in 02rgd.in 03fad.in 04flx.in 05vs.out
| |
| − | 01min.log 02rgd.log 03fad.log 04flx.log 05vs_scored.mol2
| |
| − | 01min.out 02rgd.out 03fad.out 04flx.out 05vs.sh
| |
| − | 01min_scored.mol2 02rgd_scored.mol2 03fad_scored.mol2 04flx.sh 05vs_slurm
| |
| − | 01min.sh 02rgd.sh 03fad.sh 05vs.in VS_library_005.mol2
| |
| − | (base) [ehspector@milan1 004_dock]$ cd ..
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/004_dock/05vs.in 007_virtual_screen/
| |
| − | (base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ ls
| |
| − | 05vs.in
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ mv 05vs.in virtual.in
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ ls
| |
| − | virtual.in
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ cd
| |
| − | (base) [ehspector@milan1 ~]$ cd ../../
| |
| − | (base) [ehspector@milan1 gpfs]$ cd AMS536
| |
| − | -bash: cd: AMS536: No such file or directory
| |
| − | (base) [ehspector@milan1 gpfs]$ cd projects/AMS536
| |
| − | (base) [ehspector@milan1 AMS536]$ ls
| |
| − | 1EVE_Lig_nH.mol2 1eve_Rec_nH.mol2 2018 2021 2024 junk.txt
| |
| − | 1EVE_Lig_wH.mol2 1eve_Rec_wH.mol2 2019 2022 2025 zzz.anchors
| |
| − | 1EVE_Rec_nHDMS.dms 2017 2020 2023 get_anchors.py zzz.programs
| |
| − | (base) [ehspector@milan1 AMS536]$ cd 2025
| |
| − | (base) [ehspector@milan1 2025]$ cd ..
| |
| − | (base) [ehspector@milan1 AMS536]$ cd zzz.programs/
| |
| − | (base) [ehspector@milan1 zzz.programs]$ ls
| |
| − | amber16 dock6.11 dock6-master.zip plot_footprint_single_magnitude.py
| |
| − | de_novo_anchors dock6.11_alpha dock_directory_arch plot_rmsds_amber
| |
| − | dock6.10 dock6.12 gen-frags-12 VS_libraries
| |
| − | dock6.10_milan dock6.12_ams536 old
| |
| − | (base) [ehspector@milan1 zzz.programs]$ cd VS_libraries/
| |
| − | (base) [ehspector@milan1 VS_libraries]$ ls
| |
| − | VS_library_100.mol2 VS_library_25K.mol2 VS_library_5K.mol2
| |
| − | (base) [ehspector@milan1 VS_libraries]$ pwd
| |
| − | /gpfs/projects/AMS536/zzz.programs/VS_libraries
| |
| − | (base) [ehspector@milan1 VS_libraries]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_new_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ cd ../006_footprint/
| |
| − | (base) [ehspector@milan1 006_footprint]$ ls
| |
| − | 2w26_footprint_scored.txt 2w26_hbond_scored.txt footprint.in
| |
| − | 2w26_footprint_scored.txt.pdf 2w26_scored.mol2 foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ cd ../007_virtual_screen/
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ ls
| |
| − | virtual.in
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ ls
| |
| − | 000_test 001_structure 002_spheres 003_grid 004_dock 005_analysis 006_ga_lib 007_ga_run1
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd 005_analysis/
| |
| − | (base) [ehspector@milan1 005_analysis]$ ls
| |
| − | 01fps_footprint_scored.txt 01fps_hbond_scored.txt 01fps.log1 01fps.out 01fps.sh
| |
| − | 01fps_footprint_scored.txt.pdf 01fps.in 01fps.log2 01fps_scored.mol2
| |
| − | (base) [ehspector@milan1 005_analysis]$ cd ..
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd 004_dock/
| |
| − | (base) [ehspector@milan1 004_dock]$ ls
| |
| − | 01min.in 02rgd.in 03fad.in 04flx.in 05vs.out
| |
| − | 01min.log 02rgd.log 03fad.log 04flx.log 05vs_scored.mol2
| |
| − | 01min.out 02rgd.out 03fad.out 04flx.out 05vs.sh
| |
| − | 01min_scored.mol2 02rgd_scored.mol2 03fad_scored.mol2 04flx.sh 05vs_slurm
| |
| − | 01min.sh 02rgd.sh 03fad.sh 05vs.in VS_library_005.mol2
| |
| − | (base) [ehspector@milan1 004_dock]$ vi 05vs.sh
| |
| − | (base) [ehspector@milan1 004_dock]$ vi 05vs.sh
| |
| − | (base) [ehspector@milan1 004_dock]$ cd ..
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_new_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ ls
| |
| − | virtual.in virtual.slurm
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ avail
| |
| − | PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
| |
| − | a100 up 8:00:00 1 mix@ a100-02
| |
| − | a100 up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100 up 8:00:00 1 drain* a100-01
| |
| − | a100 up 8:00:00 4 mix a100-[03-05,11]
| |
| − | a100 up 8:00:00 3 alloc a100-[06,08,10]
| |
| − | a100-large up 8:00:00 1 mix@ a100-02
| |
| − | a100-large up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-large up 8:00:00 1 drain* a100-01
| |
| − | a100-large up 8:00:00 4 mix a100-[03-05,11]
| |
| − | a100-large up 8:00:00 3 alloc a100-[06,08,10]
| |
| − | a100-long up 2-00:00:00 1 mix@ a100-02
| |
| − | a100-long up 2-00:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-long up 2-00:00:00 1 drain* a100-01
| |
| − | a100-long up 2-00:00:00 4 mix a100-[03-05,11]
| |
| − | a100-long up 2-00:00:00 3 alloc a100-[06,08,10]
| |
| − | debug-40core up 1:00:00 3 plnd dn[032,040,049]
| |
| − | debug-40core up 1:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | debug-40core up 1:00:00 2 drain* dn[031,037]
| |
| − | debug-40core up 1:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | debug-40core up 1:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | extended-40core up 7-00:00:00 3 plnd dn[032,040,049]
| |
| − | extended-40core up 7-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | extended-40core up 7-00:00:00 2 drain* dn[031,037]
| |
| − | extended-40core up 7-00:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | extended-40core up 7-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | extended-40core-shared up 3-12:00:00 3 plnd dn[032,040,049]
| |
| − | extended-40core-shared up 3-12:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | extended-40core-shared up 3-12:00:00 2 drain* dn[031,037]
| |
| − | extended-40core-shared up 3-12:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | extended-40core-shared up 3-12:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | extended-96core up 7-00:00:00 1 mix@ dg040
| |
| − | extended-96core up 7-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | extended-96core up 7-00:00:00 1 mix dg023
| |
| − | extended-96core up 7-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | extended-96core-shared up 3-12:00:00 1 mix@ dg040
| |
| − | extended-96core-shared up 3-12:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | extended-96core-shared up 3-12:00:00 1 mix dg023
| |
| − | extended-96core-shared up 3-12:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 alloc@ xm048
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 alloc xm045
| |
| − | hbm-1tb-long-96core up 2-00:00:00 2 idle xm[046-047]
| |
| − | hbm-extended-96core up 7-00:00:00 14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
| |
| − | hbm-extended-96core up 7-00:00:00 1 drain xm017
| |
| − | hbm-extended-96core up 7-00:00:00 75 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-large-96core up 8:00:00 14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
| |
| − | hbm-large-96core up 8:00:00 1 drain xm017
| |
| − | hbm-large-96core up 8:00:00 75 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-long-96core up 2-00:00:00 14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
| |
| − | hbm-long-96core up 2-00:00:00 1 drain xm017
| |
| − | hbm-long-96core up 2-00:00:00 75 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-medium-96core up 12:00:00 14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
| |
| − | hbm-medium-96core up 12:00:00 1 drain xm017
| |
| − | hbm-medium-96core up 12:00:00 75 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-short-96core up 4:00:00 14 alloc@ xm[002,004-005,008,013,015,025,027,032,039,041,044,049,051]
| |
| − | hbm-short-96core up 4:00:00 1 drain xm017
| |
| − | hbm-short-96core up 4:00:00 75 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-094]
| |
| − | large-40core up 8:00:00 3 plnd dn[032,040,049]
| |
| − | large-40core up 8:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | large-40core up 8:00:00 2 drain* dn[031,037]
| |
| − | large-40core up 8:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | large-40core up 8:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | large-96core up 8:00:00 1 mix@ dg040
| |
| − | large-96core up 8:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | large-96core up 8:00:00 1 mix dg023
| |
| − | large-96core up 8:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | long-40core up 2-00:00:00 3 plnd dn[032,040,049]
| |
| − | long-40core up 2-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | long-40core up 2-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core up 2-00:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | long-40core up 2-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | long-40core-shared up 1-00:00:00 3 plnd dn[032,040,049]
| |
| − | long-40core-shared up 1-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | long-40core-shared up 1-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core-shared up 1-00:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | long-40core-shared up 1-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | long-96core up 2-00:00:00 1 mix@ dg040
| |
| − | long-96core up 2-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | long-96core up 2-00:00:00 1 mix dg023
| |
| − | long-96core up 2-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | long-96core-shared up 1-00:00:00 1 mix@ dg040
| |
| − | long-96core-shared up 1-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | long-96core-shared up 1-00:00:00 1 mix dg023
| |
| − | long-96core-shared up 1-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | medium-40core up 12:00:00 3 plnd dn[032,040,049]
| |
| − | medium-40core up 12:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | medium-40core up 12:00:00 2 drain* dn[031,037]
| |
| − | medium-40core up 12:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | medium-40core up 12:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | medium-96core up 12:00:00 1 mix@ dg040
| |
| − | medium-96core up 12:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | medium-96core up 12:00:00 1 mix dg023
| |
| − | medium-96core up 12:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | ood-short-96core up 4:00:00 1 alloc dg038
| |
| − | rn-long-40core up 8-08:00:00 12 idle rn[001-012]
| |
| − | short-40core up 4:00:00 3 plnd dn[032,040,049]
| |
| − | short-40core up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | short-40core up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core up 4:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | short-40core up 4:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | short-40core-shared up 4:00:00 3 plnd dn[032,040,049]
| |
| − | short-40core-shared up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | short-40core-shared up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core-shared up 4:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | short-40core-shared up 4:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | short-96core up 4:00:00 1 mix@ dg040
| |
| − | short-96core up 4:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | short-96core up 4:00:00 1 mix dg023
| |
| − | short-96core up 4:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | short-96core-shared up 4:00:00 1 mix@ dg040
| |
| − | short-96core-shared up 4:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | short-96core-shared up 4:00:00 1 mix dg023
| |
| − | short-96core-shared up 4:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ ls
| |
| − | virtual.in virtual.slurm
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.in
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.slurm
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.slurm
| |
| − | sbatch: error: QOSMaxNodePerJobLimit
| |
| − | sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ mv virtual.slurm virtual.sh
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh
| |
| − | sbatch: error: QOSMaxNodePerJobLimit
| |
| − | sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh
| |
| − | Submitted batch job 927425
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927425 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Resources)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927425 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Resources)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927425 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Resources)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927425 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Resources)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927425 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Resources)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927425 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927425 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927425 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927425 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan1 ~]$ avail
| |
| − | PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
| |
| − | a100 up 8:00:00 1 mix@ a100-02
| |
| − | a100 up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100 up 8:00:00 1 drain* a100-01
| |
| − | a100 up 8:00:00 4 mix a100-[03-05,11]
| |
| − | a100 up 8:00:00 3 alloc a100-[06,08,10]
| |
| − | a100-large up 8:00:00 1 mix@ a100-02
| |
| − | a100-large up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-large up 8:00:00 1 drain* a100-01
| |
| − | a100-large up 8:00:00 4 mix a100-[03-05,11]
| |
| − | a100-large up 8:00:00 3 alloc a100-[06,08,10]
| |
| − | a100-long up 2-00:00:00 1 mix@ a100-02
| |
| − | a100-long up 2-00:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-long up 2-00:00:00 1 drain* a100-01
| |
| − | a100-long up 2-00:00:00 4 mix a100-[03-05,11]
| |
| − | a100-long up 2-00:00:00 3 alloc a100-[06,08,10]
| |
| − | debug-40core up 1:00:00 3 plnd dn[032,040,049]
| |
| − | debug-40core up 1:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | debug-40core up 1:00:00 2 drain* dn[031,037]
| |
| − | debug-40core up 1:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | debug-40core up 1:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | extended-40core up 7-00:00:00 3 plnd dn[032,040,049]
| |
| − | extended-40core up 7-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | extended-40core up 7-00:00:00 2 drain* dn[031,037]
| |
| − | extended-40core up 7-00:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | extended-40core up 7-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | extended-40core-shared up 3-12:00:00 3 plnd dn[032,040,049]
| |
| − | extended-40core-shared up 3-12:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | extended-40core-shared up 3-12:00:00 2 drain* dn[031,037]
| |
| − | extended-40core-shared up 3-12:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | extended-40core-shared up 3-12:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | extended-96core up 7-00:00:00 1 mix@ dg040
| |
| − | extended-96core up 7-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | extended-96core up 7-00:00:00 1 mix dg023
| |
| − | extended-96core up 7-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | extended-96core-shared up 3-12:00:00 1 mix@ dg040
| |
| − | extended-96core-shared up 3-12:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | extended-96core-shared up 3-12:00:00 1 mix dg023
| |
| − | extended-96core-shared up 3-12:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 alloc@ xm048
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 alloc xm045
| |
| − | hbm-1tb-long-96core up 2-00:00:00 2 idle xm[046-047]
| |
| − | hbm-extended-96core up 7-00:00:00 2 plnd xm[008,094]
| |
| − | hbm-extended-96core up 7-00:00:00 13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
| |
| − | hbm-extended-96core up 7-00:00:00 1 drain xm017
| |
| − | hbm-extended-96core up 7-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
| |
| − | hbm-large-96core up 8:00:00 2 plnd xm[008,094]
| |
| − | hbm-large-96core up 8:00:00 13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
| |
| − | hbm-large-96core up 8:00:00 1 drain xm017
| |
| − | hbm-large-96core up 8:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
| |
| − | hbm-long-96core up 2-00:00:00 2 plnd xm[008,094]
| |
| − | hbm-long-96core up 2-00:00:00 13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
| |
| − | hbm-long-96core up 2-00:00:00 1 drain xm017
| |
| − | hbm-long-96core up 2-00:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
| |
| − | hbm-medium-96core up 12:00:00 2 plnd xm[008,094]
| |
| − | hbm-medium-96core up 12:00:00 13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
| |
| − | hbm-medium-96core up 12:00:00 1 drain xm017
| |
| − | hbm-medium-96core up 12:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
| |
| − | hbm-short-96core up 4:00:00 2 plnd xm[008,094]
| |
| − | hbm-short-96core up 4:00:00 13 alloc@ xm[002,004-005,013,015,025,027,032,039,041,044,049,051]
| |
| − | hbm-short-96core up 4:00:00 1 drain xm017
| |
| − | hbm-short-96core up 4:00:00 74 alloc xm[001,003,006-007,009-012,014,016,018-024,026,028-031,033-038,040,042-043,050,052-093]
| |
| − | large-40core up 8:00:00 3 plnd dn[032,040,049]
| |
| − | large-40core up 8:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | large-40core up 8:00:00 2 drain* dn[031,037]
| |
| − | large-40core up 8:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | large-40core up 8:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | large-96core up 8:00:00 1 mix@ dg040
| |
| − | large-96core up 8:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | large-96core up 8:00:00 1 mix dg023
| |
| − | large-96core up 8:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | long-40core up 2-00:00:00 3 plnd dn[032,040,049]
| |
| − | long-40core up 2-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | long-40core up 2-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core up 2-00:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | long-40core up 2-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | long-40core-shared up 1-00:00:00 3 plnd dn[032,040,049]
| |
| − | long-40core-shared up 1-00:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | long-40core-shared up 1-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core-shared up 1-00:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | long-40core-shared up 1-00:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | long-96core up 2-00:00:00 1 mix@ dg040
| |
| − | long-96core up 2-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | long-96core up 2-00:00:00 1 mix dg023
| |
| − | long-96core up 2-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | long-96core-shared up 1-00:00:00 1 mix@ dg040
| |
| − | long-96core-shared up 1-00:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | long-96core-shared up 1-00:00:00 1 mix dg023
| |
| − | long-96core-shared up 1-00:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | medium-40core up 12:00:00 3 plnd dn[032,040,049]
| |
| − | medium-40core up 12:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | medium-40core up 12:00:00 2 drain* dn[031,037]
| |
| − | medium-40core up 12:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | medium-40core up 12:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | medium-96core up 12:00:00 1 mix@ dg040
| |
| − | medium-96core up 12:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | medium-96core up 12:00:00 1 mix dg023
| |
| − | medium-96core up 12:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | ood-short-96core up 4:00:00 1 idle dg038
| |
| − | rn-long-40core up 8-08:00:00 12 idle rn[001-012]
| |
| − | short-40core up 4:00:00 3 plnd dn[032,040,049]
| |
| − | short-40core up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | short-40core up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core up 4:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | short-40core up 4:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | short-40core-shared up 4:00:00 3 plnd dn[032,040,049]
| |
| − | short-40core-shared up 4:00:00 7 alloc@ dn[009,026,029,033,035,038,045]
| |
| − | short-40core-shared up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core-shared up 4:00:00 8 mix dn[001,003-005,007,018,027,051]
| |
| − | short-40core-shared up 4:00:00 42 alloc dn[002,006,008,010-017,019-025,028,030,034,036,039,041-044,046-048,050,052-062]
| |
| − | short-96core up 4:00:00 1 mix@ dg040
| |
| − | short-96core up 4:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | short-96core up 4:00:00 1 mix dg023
| |
| − | short-96core up 4:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | short-96core-shared up 4:00:00 1 mix@ dg040
| |
| − | short-96core-shared up 4:00:00 16 alloc@ dg[006,008-011,013,015,024,028-029,033-034,037,039,043-044]
| |
| − | short-96core-shared up 4:00:00 1 mix dg023
| |
| − | short-96core-shared up 4:00:00 29 alloc dg[001-005,007,012,014,016-022,025-027,030-032,035-036,041-042,045-048]
| |
| − | (base) [ehspector@milan1 ~]$ ls
| |
| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_new_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_new_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927425 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan1 2w26]$ scancel 927425
| |
| − | (base) [ehspector@milan1 2w26]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | (base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ ls
| |
| − | virtual.in virtual.sh
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ sbatch virtual.sh
| |
| − | Submitted batch job 927435
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/footprint.in 5EEN/006_footprint/footprint.in
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/foot.sh 5EEN/006_footprint/foot.sh
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/foot.sh 1O86/006_footprint/foot.sh
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/006_footprint/footprint.in 1O86/006_footprint/footprint.in
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 5EEN/006_footprint/
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi footprint.in
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ module load python
| |
| − | (base) [ehspector@milan1 006_footprint]$ cd ../001_structure/
| |
| − | (base) [ehspector@milan1 001_structure]$ ls
| |
| − | 5een_H_cH.mol2 5een_ligand_H_cH.mol2 5een_ligand_noH_nocH.mol2 5een_noH_nocH.mol2
| |
| − | (base) [ehspector@milan1 001_structure]$ cd ../006_footprint/
| |
| − | (base) [ehspector@milan1 006_footprint]$ bash foot.sh
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type rigid
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy no
| |
| − |
| |
| − | Molecule Library Input Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_atom_file ../004_energymin/5een.lig.min_scored.mol2
| |
| − | limit_max_ligands no
| |
| − | skip_molecule no
| |
| − | read_mol_solvation no
| |
| − | calculate_rmsd no
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter no
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand no
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter no
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules yes
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary no
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary no
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | gist_score_primary no
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | multigrid_score_primary no
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | dock3.5_score_primary no
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | continuous_score_primary no
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | footprint_similarity_score_primary yes
| |
| − | fps_score_use_footprint_reference_mol2 yes
| |
| − | fps_score_footprint_reference_mol2_filename ../001_structure/5een_ligand_H_cH.mol2
| |
| − | fps_score_foot_compare_type Euclidean
| |
| − | -------------------------------------------------------------
| |
| − | You chose to use the Euclidean distance as the metric
| |
| − | to compare the footprints. When the value is 0 then
| |
| − | there is perfect agreement between the two footprints.
| |
| − | As the agreement gets worse between the two
| |
| − | footprints the value increases.
| |
| − | -------------------------------------------------------------
| |
| − | fps_score_normalize_foot no
| |
| − | fps_score_foot_comp_all_residue yes
| |
| − | fps_score_receptor_filename ../001_structure/5een_protein_H_cH.mol2
| |
| − | fps_score_vdw_att_exp 6
| |
| − | fps_score_vdw_rep_exp 9
| |
| − | fps_score_vdw_rep_rad_scale 1
| |
| − | fps_score_use_distance_dependent_dielectric yes
| |
| − | fps_score_dielectric 4.0
| |
| − | fps_score_vdw_fp_scale 1
| |
| − | fps_score_es_fp_scale 1
| |
| − | fps_score_hb_fp_scale 0
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand no
| |
| − | simplex_final_min no
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model all
| |
| − | vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
| |
| − | flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
| |
| − | flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
| |
| − |
| |
| − | Molecule Library Output Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_outfile_prefix 5een
| |
| − | write_mol_solvation no
| |
| − | write_footprints yes
| |
| − | write_hbonds yes
| |
| − | write_orientations no
| |
| − | num_scored_conformers 1
| |
| − | score_threshold 100.0
| |
| − | rank_ligands no
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | Initializing Library File Routines...
| |
| − |
| |
| − | To cite Footprint Similarity Score use:
| |
| − | Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
| |
| − |
| |
| − | Error Opening Receptor File!
| |
| − | Traceback (most recent call last):
| |
| − | File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 211, in <module>
| |
| − | main()
| |
| − | File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 198, in main
| |
| − | (resindex_selected, resindex_remainder) = identify_residues(filename, max_res)
| |
| − | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| |
| − | File "/gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py", line 56, in identify_residues
| |
| − | resindex_selected.append(fp_array[(num_res-1)-i][0])
| |
| − | 12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])^^^^^^^^^^^^^^^
| |
| − | IndexError: list index out of range
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi footprint.in
| |
| − | (base) [ehspector@milan1 006_footprint]$ bash foot.sh
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type rigid
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy no
| |
| − |
| |
| − | Molecule Library Input Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_atom_file ../004_energymin/5een.lig.min_scored.mol2
| |
| − | limit_max_ligands no
| |
| − | skip_molecule no
| |
| − | read_mol_solvation no
| |
| − | calculate_rmsd no
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter no
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand no
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter no
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules yes
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary no
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary no
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | gist_score_primary no
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | multigrid_score_primary no
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | dock3.5_score_primary no
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | continuous_score_primary no
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | footprint_similarity_score_primary yes
| |
| − | fps_score_use_footprint_reference_mol2 yes
| |
| − | fps_score_footprint_reference_mol2_filename ../001_structure/5een_ligand_H_cH.mol2
| |
| − | fps_score_foot_compare_type Euclidean
| |
| − | -------------------------------------------------------------
| |
| − | You chose to use the Euclidean distance as the metric
| |
| − | to compare the footprints. When the value is 0 then
| |
| − | there is perfect agreement between the two footprints.
| |
| − | As the agreement gets worse between the two
| |
| − | footprints the value increases.
| |
| − | -------------------------------------------------------------
| |
| − | fps_score_normalize_foot no
| |
| − | fps_score_foot_comp_all_residue yes
| |
| − | fps_score_receptor_filename ../001_structure/5een_H_cH.mol2
| |
| − | fps_score_vdw_att_exp 6
| |
| − | fps_score_vdw_rep_exp 9
| |
| − | fps_score_vdw_rep_rad_scale 1
| |
| − | fps_score_use_distance_dependent_dielectric yes
| |
| − | fps_score_dielectric 4.0
| |
| − | fps_score_vdw_fp_scale 1
| |
| − | fps_score_es_fp_scale 1
| |
| − | fps_score_hb_fp_scale 0
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand no
| |
| − | simplex_final_min no
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model all
| |
| − | vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
| |
| − | flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
| |
| − | flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
| |
| − |
| |
| − | Molecule Library Output Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_outfile_prefix 5een
| |
| − | write_mol_solvation no
| |
| − | write_footprints yes
| |
| − | write_hbonds yes
| |
| − | write_orientations no
| |
| − | num_scored_conformers 1
| |
| − | score_threshold 100.0
| |
| − | rank_ligands no
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | Initializing Library File Routines...
| |
| − |
| |
| − | To cite Footprint Similarity Score use:
| |
| − | Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
| |
| − |
| |
| − | WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 3018
| |
| − | WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 5500
| |
| − | WARNING assign_vdw_labels: Atom valence violated for 5een.pdb atom number: 5501
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type K in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − |
| |
| − | -----------------------------------
| |
| − | Molecule: 5een.pdb
| |
| − |
| |
| − | Elapsed time for docking: 0.008 seconds
| |
| − |
| |
| − | Anchors: 1
| |
| − | Orientations: 1
| |
| − | Conformations: 1
| |
| − |
| |
| − | Footprint_Similarity_Score: 10.378089
| |
| − | FPS_vdw_energy: -39.542568
| |
| − | FPS_es_energy: -11.422824
| |
| − | FPS_vdw+es_energy: -50.965393
| |
| − | FPS_num_hbond: 2
| |
| − | FPS_vdw_fps: 8.225544
| |
| − | FPS_es_fps: 2.152545
| |
| − | FPS_hb_fps: 0.000000
| |
| − | FPS_vdw_fp_numres: 362
| |
| − | FPS_es_fp_numres: 362
| |
| − | FPS_hb_fp_numres: 362
| |
| − |
| |
| − |
| |
| − | 1 Molecules Processed
| |
| − | Total elapsed time: 0.778 seconds
| |
| − | Number of molecules per second: 1.285
| |
| − | Virtual memory used for this process: 80616 kilobytes
| |
| − | Physical memory used for this process: 9196 kilobytes
| |
| − | No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
| |
| − | /gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
| |
| − | plt.show()
| |
| − | (base) [ehspector@milan1 006_footprint]$ ls
| |
| − | 5een_footprint_scored.txt 5een_hbond_scored.txt footprint.in
| |
| − | 5een_footprint_scored.txt.pdf 5een_scored.mol2 foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ cd ..
| |
| − | (base) [ehspector@milan1 5EEN]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 1O86/001_structure/
| |
| − | (base) [ehspector@milan1 001_structure]$ ls
| |
| − | 1O86_ligand_H_cH.mol2 1O86_ligand_noH_nocH.mol2 1O86_protein_H_cH.mol2 1O86_protein_noH_nocH.mol2
| |
| − | (base) [ehspector@milan1 001_structure]$ cd ../006_footprint/
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi footprint.in
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ vi foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ bash foot.sh
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type rigid
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy no
| |
| − |
| |
| − | Molecule Library Input Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_atom_file ../004_energymin/1O86.lig.min_scored.mol2
| |
| − | limit_max_ligands no
| |
| − | skip_molecule no
| |
| − | read_mol_solvation no
| |
| − | calculate_rmsd no
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter no
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand no
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter no
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules yes
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary no
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary no
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | gist_score_primary no
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | multigrid_score_primary no
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | dock3.5_score_primary no
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | continuous_score_primary no
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | footprint_similarity_score_primary yes
| |
| − | fps_score_use_footprint_reference_mol2 yes
| |
| − | fps_score_footprint_reference_mol2_filename ../001_structure/1O86_ligand_H_cH.mol2
| |
| − | fps_score_foot_compare_type Euclidean
| |
| − | -------------------------------------------------------------
| |
| − | You chose to use the Euclidean distance as the metric
| |
| − | to compare the footprints. When the value is 0 then
| |
| − | there is perfect agreement between the two footprints.
| |
| − | As the agreement gets worse between the two
| |
| − | footprints the value increases.
| |
| − | -------------------------------------------------------------
| |
| − | fps_score_normalize_foot no
| |
| − | fps_score_foot_comp_all_residue yes
| |
| − | fps_score_receptor_filename ../001_structure/1O86_protein_H_cH.mol2
| |
| − | fps_score_vdw_att_exp 6
| |
| − | fps_score_vdw_rep_exp 9
| |
| − | fps_score_vdw_rep_rad_scale 1
| |
| − | fps_score_use_distance_dependent_dielectric yes
| |
| − | fps_score_dielectric 4.0
| |
| − | fps_score_vdw_fp_scale 1
| |
| − | fps_score_es_fp_scale 1
| |
| − | fps_score_hb_fp_scale 0
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand no
| |
| − | simplex_final_min no
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model all
| |
| − | vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
| |
| − | flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
| |
| − | flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
| |
| − |
| |
| − | Molecule Library Output Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ligand_outfile_prefix 1O86
| |
| − | write_mol_solvation no
| |
| − | write_footprints yes
| |
| − | write_hbonds yes
| |
| − | write_orientations no
| |
| − | num_scored_conformers 1
| |
| − | score_threshold 100.0
| |
| − | rank_ligands no
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | Initializing Library File Routines...
| |
| − |
| |
| − | To cite Footprint Similarity Score use:
| |
| − | Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289.
| |
| − |
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − | Warning: atom type Zn in Fingerprint::return_atom_type not recognized
| |
| − |
| |
| − | -----------------------------------
| |
| − | Molecule: 1O86_ligand.pdb
| |
| − |
| |
| − | Elapsed time for docking: 0.019 seconds
| |
| − |
| |
| − | Anchors: 1
| |
| − | Orientations: 1
| |
| − | Conformations: 1
| |
| − |
| |
| − | Footprint_Similarity_Score: 19.990522
| |
| − | FPS_vdw_energy: -62.449921
| |
| − | FPS_es_energy: -49.059299
| |
| − | FPS_vdw+es_energy: -111.509216
| |
| − | FPS_num_hbond: 4
| |
| − | FPS_vdw_fps: 4.596808
| |
| − | FPS_es_fps: 15.393714
| |
| − | FPS_hb_fps: 1.000000
| |
| − | FPS_vdw_fp_numres: 582
| |
| − | FPS_es_fp_numres: 582
| |
| − | FPS_hb_fp_numres: 582
| |
| − |
| |
| − |
| |
| − | 1 Molecules Processed
| |
| − | Total elapsed time: 2.107 seconds
| |
| − | Number of molecules per second: 0.475
| |
| − | Virtual memory used for this process: 83536 kilobytes
| |
| − | Physical memory used for this process: 11424 kilobytes
| |
| − | No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
| |
| − | /gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py:170: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
| |
| − | plt.show()
| |
| − | (base) [ehspector@milan1 006_footprint]$ ls
| |
| − | 1O86_footprint_scored.txt 1O86_hbond_scored.txt footprint.in
| |
| − | 1O86_footprint_scored.txt.pdf 1O86_scored.mol2 foot.sh
| |
| − | (base) [ehspector@milan1 006_footprint]$ cd ..
| |
| − | (base) [ehspector@milan1 1O86]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.in 5EEN/007_virtualscreen/virtual.in
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.sh 5EEN/007_virtualscreen/virtual.sh
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan1 AMS_536]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.sh 1O86/007_virtualscreen/virtual.sh
| |
| − | (base) [ehspector@milan1 Tutorials]$ cp 2w26/007_virtual_screen/virtual.in 1O86/007_virtualscreen/virtual.in
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan2 ~]$ avail
| |
| − | PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
| |
| − | a100 up 8:00:00 1 mix@ a100-02
| |
| − | a100 up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100 up 8:00:00 1 drain* a100-01
| |
| − | a100 up 8:00:00 2 mix a100-[03,05]
| |
| − | a100 up 8:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | a100-large up 8:00:00 1 mix@ a100-02
| |
| − | a100-large up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-large up 8:00:00 1 drain* a100-01
| |
| − | a100-large up 8:00:00 2 mix a100-[03,05]
| |
| − | a100-large up 8:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | a100-long up 2-00:00:00 1 mix@ a100-02
| |
| − | a100-long up 2-00:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-long up 2-00:00:00 1 drain* a100-01
| |
| − | a100-long up 2-00:00:00 2 mix a100-[03,05]
| |
| − | a100-long up 2-00:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | debug-40core up 1:00:00 3 plnd dn[050,061-062]
| |
| − | debug-40core up 1:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | debug-40core up 1:00:00 2 drain* dn[031,037]
| |
| − | debug-40core up 1:00:00 4 mix dn[004-005,018,051]
| |
| − | debug-40core up 1:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | extended-40core up 7-00:00:00 3 plnd dn[050,061-062]
| |
| − | extended-40core up 7-00:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | extended-40core up 7-00:00:00 2 drain* dn[031,037]
| |
| − | extended-40core up 7-00:00:00 4 mix dn[004-005,018,051]
| |
| − | extended-40core up 7-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | extended-40core-shared up 3-12:00:00 3 plnd dn[050,061-062]
| |
| − | extended-40core-shared up 3-12:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | extended-40core-shared up 3-12:00:00 2 drain* dn[031,037]
| |
| − | extended-40core-shared up 3-12:00:00 4 mix dn[004-005,018,051]
| |
| − | extended-40core-shared up 3-12:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | extended-96core up 7-00:00:00 1 mix@ dg040
| |
| − | extended-96core up 7-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | extended-96core up 7-00:00:00 2 mix dg[009,023]
| |
| − | extended-96core up 7-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
| |
| − | extended-96core up 7-00:00:00 3 idle dg[032,035-036]
| |
| − | extended-96core-shared up 3-12:00:00 1 mix@ dg040
| |
| − | extended-96core-shared up 3-12:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | extended-96core-shared up 3-12:00:00 2 mix dg[009,023]
| |
| − | extended-96core-shared up 3-12:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
| |
| − | extended-96core-shared up 3-12:00:00 3 idle dg[032,035-036]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 3 alloc xm[045-047]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 idle xm048
| |
| − | hbm-extended-96core up 7-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-extended-96core up 7-00:00:00 1 drain xm017
| |
| − | hbm-extended-96core up 7-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-large-96core up 8:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-large-96core up 8:00:00 1 drain xm017
| |
| − | hbm-large-96core up 8:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-long-96core up 2-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-long-96core up 2-00:00:00 1 drain xm017
| |
| − | hbm-long-96core up 2-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-medium-96core up 12:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-medium-96core up 12:00:00 1 drain xm017
| |
| − | hbm-medium-96core up 12:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-short-96core up 4:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-short-96core up 4:00:00 1 drain xm017
| |
| − | hbm-short-96core up 4:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | large-40core up 8:00:00 3 plnd dn[050,061-062]
| |
| − | large-40core up 8:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | large-40core up 8:00:00 2 drain* dn[031,037]
| |
| − | large-40core up 8:00:00 4 mix dn[004-005,018,051]
| |
| − | large-40core up 8:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | large-96core up 8:00:00 1 mix@ dg040
| |
| − | large-96core up 8:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | large-96core up 8:00:00 2 mix dg[009,023]
| |
| − | large-96core up 8:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
| |
| − | large-96core up 8:00:00 3 idle dg[032,035-036]
| |
| − | long-40core up 2-00:00:00 3 plnd dn[050,061-062]
| |
| − | long-40core up 2-00:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | long-40core up 2-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core up 2-00:00:00 4 mix dn[004-005,018,051]
| |
| − | long-40core up 2-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | long-40core-shared up 1-00:00:00 3 plnd dn[050,061-062]
| |
| − | long-40core-shared up 1-00:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | long-40core-shared up 1-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core-shared up 1-00:00:00 4 mix dn[004-005,018,051]
| |
| − | long-40core-shared up 1-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | long-96core up 2-00:00:00 1 mix@ dg040
| |
| − | long-96core up 2-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | long-96core up 2-00:00:00 2 mix dg[009,023]
| |
| − | long-96core up 2-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
| |
| − | long-96core up 2-00:00:00 3 idle dg[032,035-036]
| |
| − | long-96core-shared up 1-00:00:00 1 mix@ dg040
| |
| − | long-96core-shared up 1-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | long-96core-shared up 1-00:00:00 2 mix dg[009,023]
| |
| − | long-96core-shared up 1-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
| |
| − | long-96core-shared up 1-00:00:00 3 idle dg[032,035-036]
| |
| − | medium-40core up 12:00:00 3 plnd dn[050,061-062]
| |
| − | medium-40core up 12:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | medium-40core up 12:00:00 2 drain* dn[031,037]
| |
| − | medium-40core up 12:00:00 4 mix dn[004-005,018,051]
| |
| − | medium-40core up 12:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | medium-96core up 12:00:00 1 mix@ dg040
| |
| − | medium-96core up 12:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | medium-96core up 12:00:00 2 mix dg[009,023]
| |
| − | medium-96core up 12:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
| |
| − | medium-96core up 12:00:00 3 idle dg[032,035-036]
| |
| − | ood-short-96core up 4:00:00 1 idle dg038
| |
| − | rn-long-40core up 8-08:00:00 12 idle rn[001-012]
| |
| − | short-40core up 4:00:00 3 plnd dn[050,061-062]
| |
| − | short-40core up 4:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | short-40core up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core up 4:00:00 4 mix dn[004-005,018,051]
| |
| − | short-40core up 4:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | short-40core-shared up 4:00:00 3 plnd dn[050,061-062]
| |
| − | short-40core-shared up 4:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | short-40core-shared up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core-shared up 4:00:00 4 mix dn[004-005,018,051]
| |
| − | short-40core-shared up 4:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | short-96core up 4:00:00 1 mix@ dg040
| |
| − | short-96core up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | short-96core up 4:00:00 2 mix dg[009,023]
| |
| − | short-96core up 4:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
| |
| − | short-96core up 4:00:00 3 idle dg[032,035-036]
| |
| − | short-96core-shared up 4:00:00 1 mix@ dg040
| |
| − | short-96core-shared up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | short-96core-shared up 4:00:00 2 mix dg[009,023]
| |
| − | short-96core-shared up 4:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-031,037,039,041-042,044-048]
| |
| − | short-96core-shared up 4:00:00 3 idle dg[032,035-036]
| |
| − | (base) [ehspector@milan2 ~]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 927435 ood-short 2w26_vs_ ehspecto PD 0:00 6 (PartitionConfig)
| |
| − | (base) [ehspector@milan2 ~]$ scancel 927435
| |
| − | (base) [ehspector@milan2 ~]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | (base) [ehspector@milan2 ~]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan2 2w26]$ cd 007_virtual_screen/
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ sbatch virtual.sh
| |
| − | Submitted batch job 928050
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928050 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Resources)
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928050 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Resources)
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928050 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Resources)
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928050 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Resources)
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928050 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Resources)
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928050 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928050 short-96c 2w26_vs_ ehspecto PD 0:00 6 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ scancel 928050
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ sbatch virtual.sh
| |
| − | Submitted batch job 928053
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 0:03 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 0:07 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 0:10 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 0:49 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 0:50 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:42 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 Tutorials]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:43 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/006_footprint/
| |
| − | (base) [ehspector@milan2 006_footprint]$ ls
| |
| − | 2w26_footprint_scored.txt 2w26_hbond_scored.txt footprint.in
| |
| − | 2w26_footprint_scored.txt.pdf 2w26_scored.mol2 foot.sh
| |
| − | (base) [ehspector@milan2 006_footprint]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 6:28 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 006_footprint]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 6:29 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 006_footprint]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 6:56 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 006_footprint]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 7:42 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 006_footprint]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ../5EEN/
| |
| − | (base) [ehspector@milan2 5EEN]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore
| |
| − | 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min commands.txt
| |
| − | (base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ ls
| |
| − | virtual.in virtual.sh
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ avail
| |
| − | PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
| |
| − | a100 up 8:00:00 1 mix@ a100-02
| |
| − | a100 up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100 up 8:00:00 1 drain* a100-01
| |
| − | a100 up 8:00:00 2 mix a100-[03,05]
| |
| − | a100 up 8:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | a100-large up 8:00:00 1 mix@ a100-02
| |
| − | a100-large up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-large up 8:00:00 1 drain* a100-01
| |
| − | a100-large up 8:00:00 2 mix a100-[03,05]
| |
| − | a100-large up 8:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | a100-long up 2-00:00:00 1 mix@ a100-02
| |
| − | a100-long up 2-00:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-long up 2-00:00:00 1 drain* a100-01
| |
| − | a100-long up 2-00:00:00 2 mix a100-[03,05]
| |
| − | a100-long up 2-00:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | debug-40core up 1:00:00 3 plnd dn[050,061-062]
| |
| − | debug-40core up 1:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | debug-40core up 1:00:00 2 drain* dn[031,037]
| |
| − | debug-40core up 1:00:00 4 mix dn[004-005,018,051]
| |
| − | debug-40core up 1:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | extended-40core up 7-00:00:00 3 plnd dn[050,061-062]
| |
| − | extended-40core up 7-00:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | extended-40core up 7-00:00:00 2 drain* dn[031,037]
| |
| − | extended-40core up 7-00:00:00 4 mix dn[004-005,018,051]
| |
| − | extended-40core up 7-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | extended-40core-shared up 3-12:00:00 3 plnd dn[050,061-062]
| |
| − | extended-40core-shared up 3-12:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | extended-40core-shared up 3-12:00:00 2 drain* dn[031,037]
| |
| − | extended-40core-shared up 3-12:00:00 4 mix dn[004-005,018,051]
| |
| − | extended-40core-shared up 3-12:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | extended-96core up 7-00:00:00 1 plnd dg039
| |
| − | extended-96core up 7-00:00:00 1 mix@ dg040
| |
| − | extended-96core up 7-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | extended-96core up 7-00:00:00 2 mix dg[009,023]
| |
| − | extended-96core up 7-00:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
| |
| − | extended-96core-shared up 3-12:00:00 1 plnd dg039
| |
| − | extended-96core-shared up 3-12:00:00 1 mix@ dg040
| |
| − | extended-96core-shared up 3-12:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | extended-96core-shared up 3-12:00:00 2 mix dg[009,023]
| |
| − | extended-96core-shared up 3-12:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 3 alloc xm[045-047]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 idle xm048
| |
| − | hbm-extended-96core up 7-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-extended-96core up 7-00:00:00 1 drain xm017
| |
| − | hbm-extended-96core up 7-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-large-96core up 8:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-large-96core up 8:00:00 1 drain xm017
| |
| − | hbm-large-96core up 8:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-long-96core up 2-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-long-96core up 2-00:00:00 1 drain xm017
| |
| − | hbm-long-96core up 2-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-medium-96core up 12:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-medium-96core up 12:00:00 1 drain xm017
| |
| − | hbm-medium-96core up 12:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-short-96core up 4:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-short-96core up 4:00:00 1 drain xm017
| |
| − | hbm-short-96core up 4:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | large-40core up 8:00:00 3 plnd dn[050,061-062]
| |
| − | large-40core up 8:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | large-40core up 8:00:00 2 drain* dn[031,037]
| |
| − | large-40core up 8:00:00 4 mix dn[004-005,018,051]
| |
| − | large-40core up 8:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | large-96core up 8:00:00 1 plnd dg039
| |
| − | large-96core up 8:00:00 1 mix@ dg040
| |
| − | large-96core up 8:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | large-96core up 8:00:00 2 mix dg[009,023]
| |
| − | large-96core up 8:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
| |
| − | long-40core up 2-00:00:00 3 plnd dn[050,061-062]
| |
| − | long-40core up 2-00:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | long-40core up 2-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core up 2-00:00:00 4 mix dn[004-005,018,051]
| |
| − | long-40core up 2-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | long-40core-shared up 1-00:00:00 3 plnd dn[050,061-062]
| |
| − | long-40core-shared up 1-00:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | long-40core-shared up 1-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core-shared up 1-00:00:00 4 mix dn[004-005,018,051]
| |
| − | long-40core-shared up 1-00:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | long-96core up 2-00:00:00 1 plnd dg039
| |
| − | long-96core up 2-00:00:00 1 mix@ dg040
| |
| − | long-96core up 2-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | long-96core up 2-00:00:00 2 mix dg[009,023]
| |
| − | long-96core up 2-00:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
| |
| − | long-96core-shared up 1-00:00:00 1 plnd dg039
| |
| − | long-96core-shared up 1-00:00:00 1 mix@ dg040
| |
| − | long-96core-shared up 1-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | long-96core-shared up 1-00:00:00 2 mix dg[009,023]
| |
| − | long-96core-shared up 1-00:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
| |
| − | medium-40core up 12:00:00 3 plnd dn[050,061-062]
| |
| − | medium-40core up 12:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | medium-40core up 12:00:00 2 drain* dn[031,037]
| |
| − | medium-40core up 12:00:00 4 mix dn[004-005,018,051]
| |
| − | medium-40core up 12:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | medium-96core up 12:00:00 1 plnd dg039
| |
| − | medium-96core up 12:00:00 1 mix@ dg040
| |
| − | medium-96core up 12:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | medium-96core up 12:00:00 2 mix dg[009,023]
| |
| − | medium-96core up 12:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
| |
| − | ood-short-96core up 4:00:00 1 idle dg038
| |
| − | rn-long-40core up 8-08:00:00 12 idle rn[001-012]
| |
| − | short-40core up 4:00:00 3 plnd dn[050,061-062]
| |
| − | short-40core up 4:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | short-40core up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core up 4:00:00 4 mix dn[004-005,018,051]
| |
| − | short-40core up 4:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | short-40core-shared up 4:00:00 3 plnd dn[050,061-062]
| |
| − | short-40core-shared up 4:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | short-40core-shared up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core-shared up 4:00:00 4 mix dn[004-005,018,051]
| |
| − | short-40core-shared up 4:00:00 47 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-049,052-060]
| |
| − | short-96core up 4:00:00 1 plnd dg039
| |
| − | short-96core up 4:00:00 1 mix@ dg040
| |
| − | short-96core up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | short-96core up 4:00:00 2 mix dg[009,023]
| |
| − | short-96core up 4:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
| |
| − | short-96core-shared up 4:00:00 1 plnd dg039
| |
| − | short-96core-shared up 4:00:00 1 mix@ dg040
| |
| − | short-96core-shared up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | short-96core-shared up 4:00:00 2 mix dg[009,023]
| |
| − | short-96core-shared up 4:00:00 36 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,041-042,044-048]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.in
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
| |
| − | Submitted batch job 928057
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928057 short-40c 2w26_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 12:28 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928057 short-40c 2w26_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 12:41 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928057 short-40c 2w26_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 12:46 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928057 short-40c 2w26_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 12:47 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928057 short-40c 2w26_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 12:49 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928057 short-40c 2w26_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 14:35 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928057 short-40c 2w26_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 14:38 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928057 short-40c 2w26_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 14:40 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928057 short-40c 2w26_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 14:42 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ ls
| |
| − | virtual.in virtual.sh
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928057 short-40c 2w26_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 15:00 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928057 short-40c 2w26_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 15:06 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ scancel 928057
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 16:00 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ avail
| |
| − | PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
| |
| − | a100 up 8:00:00 1 mix@ a100-02
| |
| − | a100 up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100 up 8:00:00 1 drain* a100-01
| |
| − | a100 up 8:00:00 2 mix a100-[03,05]
| |
| − | a100 up 8:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | a100-large up 8:00:00 1 mix@ a100-02
| |
| − | a100-large up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-large up 8:00:00 1 drain* a100-01
| |
| − | a100-large up 8:00:00 2 mix a100-[03,05]
| |
| − | a100-large up 8:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | a100-long up 2-00:00:00 1 mix@ a100-02
| |
| − | a100-long up 2-00:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-long up 2-00:00:00 1 drain* a100-01
| |
| − | a100-long up 2-00:00:00 2 mix a100-[03,05]
| |
| − | a100-long up 2-00:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | debug-40core up 1:00:00 2 plnd dn[061-062]
| |
| − | debug-40core up 1:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | debug-40core up 1:00:00 2 drain* dn[031,037]
| |
| − | debug-40core up 1:00:00 4 mix dn[004-005,018,051]
| |
| − | debug-40core up 1:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
| |
| − | extended-40core up 7-00:00:00 2 plnd dn[061-062]
| |
| − | extended-40core up 7-00:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | extended-40core up 7-00:00:00 2 drain* dn[031,037]
| |
| − | extended-40core up 7-00:00:00 4 mix dn[004-005,018,051]
| |
| − | extended-40core up 7-00:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
| |
| − | extended-40core-shared up 3-12:00:00 2 plnd dn[061-062]
| |
| − | extended-40core-shared up 3-12:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | extended-40core-shared up 3-12:00:00 2 drain* dn[031,037]
| |
| − | extended-40core-shared up 3-12:00:00 4 mix dn[004-005,018,051]
| |
| − | extended-40core-shared up 3-12:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
| |
| − | extended-96core up 7-00:00:00 3 plnd dg[006,026,039]
| |
| − | extended-96core up 7-00:00:00 1 mix@ dg040
| |
| − | extended-96core up 7-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | extended-96core up 7-00:00:00 2 mix dg[009,023]
| |
| − | extended-96core up 7-00:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
| |
| − | extended-96core-shared up 3-12:00:00 3 plnd dg[006,026,039]
| |
| − | extended-96core-shared up 3-12:00:00 1 mix@ dg040
| |
| − | extended-96core-shared up 3-12:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | extended-96core-shared up 3-12:00:00 2 mix dg[009,023]
| |
| − | extended-96core-shared up 3-12:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 3 alloc xm[045-047]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 idle xm048
| |
| − | hbm-extended-96core up 7-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-extended-96core up 7-00:00:00 1 drain xm017
| |
| − | hbm-extended-96core up 7-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-large-96core up 8:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-large-96core up 8:00:00 1 drain xm017
| |
| − | hbm-large-96core up 8:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-long-96core up 2-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-long-96core up 2-00:00:00 1 drain xm017
| |
| − | hbm-long-96core up 2-00:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-medium-96core up 12:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-medium-96core up 12:00:00 1 drain xm017
| |
| − | hbm-medium-96core up 12:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-short-96core up 4:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-short-96core up 4:00:00 1 drain xm017
| |
| − | hbm-short-96core up 4:00:00 79 alloc xm[001-003,006-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | large-40core up 8:00:00 2 plnd dn[061-062]
| |
| − | large-40core up 8:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | large-40core up 8:00:00 2 drain* dn[031,037]
| |
| − | large-40core up 8:00:00 4 mix dn[004-005,018,051]
| |
| − | large-40core up 8:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
| |
| − | large-96core up 8:00:00 3 plnd dg[006,026,039]
| |
| − | large-96core up 8:00:00 1 mix@ dg040
| |
| − | large-96core up 8:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | large-96core up 8:00:00 2 mix dg[009,023]
| |
| − | large-96core up 8:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
| |
| − | long-40core up 2-00:00:00 2 plnd dn[061-062]
| |
| − | long-40core up 2-00:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | long-40core up 2-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core up 2-00:00:00 4 mix dn[004-005,018,051]
| |
| − | long-40core up 2-00:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
| |
| − | long-40core-shared up 1-00:00:00 2 plnd dn[061-062]
| |
| − | long-40core-shared up 1-00:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | long-40core-shared up 1-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core-shared up 1-00:00:00 4 mix dn[004-005,018,051]
| |
| − | long-40core-shared up 1-00:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
| |
| − | long-96core up 2-00:00:00 3 plnd dg[006,026,039]
| |
| − | long-96core up 2-00:00:00 1 mix@ dg040
| |
| − | long-96core up 2-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | long-96core up 2-00:00:00 2 mix dg[009,023]
| |
| − | long-96core up 2-00:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
| |
| − | long-96core-shared up 1-00:00:00 3 plnd dg[006,026,039]
| |
| − | long-96core-shared up 1-00:00:00 1 mix@ dg040
| |
| − | long-96core-shared up 1-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | long-96core-shared up 1-00:00:00 2 mix dg[009,023]
| |
| − | long-96core-shared up 1-00:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
| |
| − | medium-40core up 12:00:00 2 plnd dn[061-062]
| |
| − | medium-40core up 12:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | medium-40core up 12:00:00 2 drain* dn[031,037]
| |
| − | medium-40core up 12:00:00 4 mix dn[004-005,018,051]
| |
| − | medium-40core up 12:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
| |
| − | medium-96core up 12:00:00 3 plnd dg[006,026,039]
| |
| − | medium-96core up 12:00:00 1 mix@ dg040
| |
| − | medium-96core up 12:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | medium-96core up 12:00:00 2 mix dg[009,023]
| |
| − | medium-96core up 12:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
| |
| − | ood-short-96core up 4:00:00 1 idle dg038
| |
| − | rn-long-40core up 8-08:00:00 12 idle rn[001-012]
| |
| − | short-40core up 4:00:00 2 plnd dn[061-062]
| |
| − | short-40core up 4:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | short-40core up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core up 4:00:00 4 mix dn[004-005,018,051]
| |
| − | short-40core up 4:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
| |
| − | short-40core-shared up 4:00:00 2 plnd dn[061-062]
| |
| − | short-40core-shared up 4:00:00 6 alloc@ dn[009,026,029,035,038,045]
| |
| − | short-40core-shared up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core-shared up 4:00:00 4 mix dn[004-005,018,051]
| |
| − | short-40core-shared up 4:00:00 48 alloc dn[001-003,006-008,010-017,019-025,027-028,030,032-034,036,039-044,046-050,052-060]
| |
| − | short-96core up 4:00:00 3 plnd dg[006,026,039]
| |
| − | short-96core up 4:00:00 1 mix@ dg040
| |
| − | short-96core up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | short-96core up 4:00:00 2 mix dg[009,023]
| |
| − | short-96core up 4:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
| |
| − | short-96core-shared up 4:00:00 3 plnd dg[006,026,039]
| |
| − | short-96core-shared up 4:00:00 1 mix@ dg040
| |
| − | short-96core-shared up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | short-96core-shared up 4:00:00 2 mix dg[009,023]
| |
| − | short-96core-shared up 4:00:00 34 alloc dg[001-005,007-008,010-012,014-022,025,027,030-032,035-037,041-042,044-048]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ cd ../
| |
| − | (base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
| |
| − | Submitted batch job 928060
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 19:15 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 19:17 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 19:18 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 19:19 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 19:38 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 19:40 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 19:41 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
| |
| − | Submitted batch job 928063
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928063 short-40c 5een_vs_ ehspecto PD 0:00 4 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 21:35 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ scancel 928063
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 21:54 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
| |
| − | sbatch: error: QOSMaxNodePerJobLimit
| |
| − | sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
| |
| − | Submitted batch job 928066
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 23:11 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 23:13 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 23:13 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 23:16 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 23:17 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 23:17 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 23:18 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 24:32 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 24:38 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 24:39 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ sbatch virtual.sh
| |
| − | Submitted batch job 928070
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 25:10 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 25:19 3 dg[032,035-036]
| |
| − | 928066 short-96c 5een_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ scancel 928066
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 25:37 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 25:50 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto PD 0:00 3 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 25:51 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@login.seawulf.stonybrook.edu
| |
| − | ehspector@login.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | ****IMPORTANT MESSAGE BELOW****
| |
| − |
| |
| − |
| |
| − | In order to allow the university to perform a generator test on the campus data center, the 28-core, Tesla k80 gpu, Tesla p100, and Tesla v100 queues and login nodes login1 and login2 will be going offline for scheduled maintenance at 4pm on Monday, February 24th. The maintenance is expected to conclude by lunch time on Tuesday, February 25th. The 40-core, 96-core, a100 gpu queues will NOT be impacted by this maintenance. Similarly, the Milan1 and Milan2 login nodes will continue to be available. We thank you for your patience while these necessary tests are conducted.
| |
| − |
| |
| − | (base) [ehspector@login2 ~]$ cd ..
| |
| − | (base) [ehspector@login2 home]$ home
| |
| − | (base) [ehspector@login2 espector]$ cd builds/alpha_branch/src/dock
| |
| − | (base) [ehspector@login2 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@login2 dock]$ cd ../../install/
| |
| − | (base) [ehspector@login2 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | amake[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@login2 install]$ make dock\
| |
| − | > ^C
| |
| − | (base) [ehspector@login2 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Thu Feb 13 11:05:05 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dock.o dock.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:778:5: error: ‘Filter’ was not declared in this scope
| |
| − | 778 | Filter filter;
| |
| − | | ^12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [dockmol.o] Error 1
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [dock] Error 2
| |
| − | (base) [ehspector@login2 install]$ cd ../../
| |
| − | (base) [ehspector@login2 builds]$ cd alpha_branch/src/dock
| |
| − | (base) [ehspector@login2 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@login2 dock]$ cd ../../
| |
| − | (base) [ehspector@login2 alpha_branch]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@login2 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@login2 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Thu Feb 13 11:07:50 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dock.o dock.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp
| |
| − | g++ -c -O2 -std=c++11 -o filter.o filter.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp
| |
| − | g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp
| |
| − | g++ -c -O2 -std=c++11 -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp
| |
| − | g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp
| |
| − | g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o orient.o orient.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score.o score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp
| |
| − | g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp
| |
| − | g++ -c -O2 -std=c++11 -o trace.o trace.cpp
| |
| − | g++ -c -O2 -std=c++11 -o utils.o utils.cpp
| |
| − | g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp
| |
| − | g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp
| |
| − | cd nab && make all
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | gcc -c -O3 -D_ANSI_SOURCE molio.c
| |
| − | gcc -c -O2 -o prm.o prm.c
| |
| − | make is_LEX_available
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c
| |
| − | gcc -c -O2 -o traceback.o traceback.c
| |
| − | gcc -c -O2 -o select_atoms.o select_atoms.c
| |
| − | gcc -c -O2 -o memutil.o memutil.c
| |
| − | gcc -c -O2 -o reslib.o reslib.c
| |
| − | gcc -c -O2 -o jacobi.o jacobi.c
| |
| − | gcc -c -O2 -o molutil.o molutil.c
| |
| − | gcc -c -O2 -o chirvol.o chirvol.c
| |
| − | gcc -c -O2 -o regexp.o regexp.c
| |
| − | gcc -c -O2 -o binpos.o binpos.c
| |
| − | gcc -c -O2 -o time.o time.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE rand2.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE conjgrad.c
| |
| − | gcc -c -O2 -o database.o database.c
| |
| − | gcc -c -O2 -o tleap.o tleap.c
| |
| − | ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
| |
| − | ar: creating nab.a
| |
| − | a - molio.o
| |
| − | a - prm.o
| |
| − | a - sff.o
| |
| − | a - traceback.o
| |
| − | a - select_atoms.o
| |
| − | a - memutil.o
| |
| − | a - reslib.o
| |
| − | a - jacobi.o
| |
| − | a - molutil.o
| |
| − | a - chirvol.o
| |
| − | a - regexp.o
| |
| − | a - binpos.o
| |
| − | a - time.o
| |
| − | a - rand2.o
| |
| − | a - conjgrad.o
| |
| − | a - database.o
| |
| − | a - tleap.o
| |
| − | ranlib nab.a
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
| |
| − | ar cr libgzstream.a gzstream.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
| |
| − | -lm -lpthread
| |
| − | mv dock6 ../../bin
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − |
| |
| − | Installation of
| |
| − | DOCK v6.12
| |
| − | (base) [ehspector@login2 install]$ cd ../
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd ../
| |
| − | (base) [ehspector@login2 builds]$ cd alpha_branch/src/dock
| |
| − | (base) [ehspector@login2 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@login2 dock]$ cd ..
| |
| − | (base) [ehspector@login2 src]$ cd ..
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@login2 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@login2 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Thu Feb 13 11:20:49 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dock.o dock.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:917:16: error: ‘class Filter’ has no member named ‘gasteiger’; did you mean ‘gasteigerize’?
| |
| − | 917 | if (filter.gasteiger){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | | gasteigerize
| |
| − | dockmol.cpp:931:5: error: jump to label ‘skip’
| |
| − | 931 | skip:
| |
| − | | ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp:918:10: note: from here
| |
| − | 918 | goto skip;
| |
| − | | ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp:919:9: note: crosses initialization of ‘int num_zeros’
| |
| − | 919 | int num_zeros = 0;
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | make[1]: *** [dockmol.o] Error 1
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [dock] Error 2
| |
| − | (base) [ehspector@login2 install]$ cd ..
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd src/dock
| |
| − | (base) [ehspector@login2 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@login2 dock]$ cd ..
| |
| − | \(base) [ehspector@login2 src]$ cd ../
| |
| − | (base) [ehspector@login2 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@login2 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@login2 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Thu Feb 13 11:25:35 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -o amber_typer.o amber_typer.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_mpi.o base_mpi.cpp
| |
| − | g++ -c -O2 -std=c++11 -o base_score.o base_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | g++ -c -O2 -std=c++11 -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dock.o dock.cpp
| |
| − | g++ -c -O2 -std=c++11 -o dockmol.o dockmol.cpp
| |
| − | g++ -c -O2 -std=c++11 -o filter.o filter.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fingerprint.o fingerprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fraggraph.o fraggraph.cpp
| |
| − | g++ -c -O2 -std=c++11 -o fragment.o fragment.cpp
| |
| − | g++ -c -O2 -std=c++11 -o gasteiger.o gasteiger.cpp
| |
| − | g++ -c -O2 -std=c++11 -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o hungarian.o hungarian.cpp
| |
| − | g++ -c -O2 -std=c++11 -o library_file.o library_file.cpp
| |
| − | g++ -c -O2 -std=c++11 -o limit_max_change.o limit_max_change.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_conf.o master_conf.cpp
| |
| − | g++ -c -O2 -std=c++11 -o master_score.o master_score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o orient.o orient.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sasa.o sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score.o score.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_amber.o score_amber.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_chemgrid.o score_chemgrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_descriptor.o score_descriptor.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_footprint.o score_footprint.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_ph4.o score_ph4.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_volume.o score_volume.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_gist.o score_gist.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_hbond.o score_hbond.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_internal.o score_internal.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_multigrid.o score_multigrid.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_sasa.o score_sasa.cpp
| |
| − | g++ -c -O2 -std=c++11 -o score_solvent.o score_solvent.cpp
| |
| − | g++ -c -O2 -std=c++11 -o simplex.o simplex.cpp
| |
| − | g++ -c -O2 -std=c++11 -o sphere.o sphere.cpp
| |
| − | g++ -c -O2 -std=c++11 -o trace.o trace.cpp
| |
| − | g++ -c -O2 -std=c++11 -o utils.o utils.cpp
| |
| − | g++ -c -O2 -std=c++11 -o iso_align.o iso_align.cpp
| |
| − | g++ -c -O2 -std=c++11 -o mem_info.o mem_info.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rdtyper.o rdtyper.cpp
| |
| − | g++ -c -O2 -std=c++11 -o rddrive.o rddrive.cpp
| |
| − | cd nab && make all
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | gcc -c -O3 -D_ANSI_SOURCE molio.c
| |
| − | gcc -c -O2 -o prm.o prm.c
| |
| − | make is_LEX_available
| |
| − | make[3]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | make[3]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c
| |
| − | gcc -c -O2 -o traceback.o traceback.c
| |
| − | gcc -c -O2 -o select_atoms.o select_atoms.c
| |
| − | gcc -c -O2 -o memutil.o memutil.c
| |
| − | gcc -c -O2 -o reslib.o reslib.c
| |
| − | gcc -c -O2 -o jacobi.o jacobi.c
| |
| − | gcc -c -O2 -o molutil.o molutil.c
| |
| − | gcc -c -O2 -o chirvol.o chirvol.c
| |
| − | gcc -c -O2 -o regexp.o regexp.c
| |
| − | gcc -c -O2 -o binpos.o binpos.c
| |
| − | gcc -c -O2 -o time.o time.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE rand2.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE conjgrad.c
| |
| − | gcc -c -O2 -o database.o database.c
| |
| − | gcc -c -O2 -o tleap.o tleap.c
| |
| − | ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
| |
| − | ar: creating nab.a
| |
| − | a - molio.o
| |
| − | a - prm.o
| |
| − | a - sff.o
| |
| − | a - traceback.o
| |
| − | a - select_atoms.o
| |
| − | a - memutil.o
| |
| − | a - reslib.o
| |
| − | a - jacobi.o
| |
| − | a - molutil.o
| |
| − | a - chirvol.o
| |
| − | a - regexp.o
| |
| − | a - binpos.o
| |
| − | a - time.o
| |
| − | a - rand2.o
| |
| − | a - conjgrad.o
| |
| − | a - database.o
| |
| − | a - tleap.o
| |
| − | ranlib nab.a
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make
| |
| − | make[2]: Entering directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -I. -O2 -std=c++11 -c -o gzstream.o gzstream.C
| |
| − | ar cr libgzstream.a gzstream.o
| |
| − | make[2]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
| |
| − | -lm -lpthread
| |
| − | mv dock6 ../../bin
| |
| − | make[1]: Leaving directory `/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − |
| |
| − | Installation of
| |
| − | DOCK v6.12
| |
| − | program dock is complete at Thu Feb 13 11:27:30 EST 2025.
| |
| − |
| |
| − | (base) [ehspector@login2 install]$ cd
| |
| − | (base) [ehspector@login2 ~]$ home
| |
| − | (base) [ehspector@login2 espector]$ cd 4s0v/gas_teiger/
| |
| − | (base) [ehspector@login2 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.out gas_5.out no_gas.in
| |
| − | 1AAQ_yesG.mol2 gas_3.out_scored.mol2 gas_5.out_scored.mol2 no_gas.out
| |
| − | gas_2.in gas_4.in gas.in no_gas.out_scored.mol2
| |
| − | gas_2.out gas_4.out gas.out test.mol2
| |
| − | gas_2.out_scored.mol2 gas_4.out_scored.mol2 gas.out_scored.mol2 test_nocharge.mol2
| |
| − | gas_3.in gas_5.in no_charge
| |
| − | (base) [ehspector@login2 gas_teiger]$ mkdir test
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_3.in
| |
| − | (base) [ehspector@login2 gas_teiger]$ mv test_nocharge.mol2 test
| |
| − | (base) [ehspector@login2 gas_teiger]$ mv gas_3.in
| |
| − | mv: missing destination file operand after ‘gas_3.in’
| |
| − | Try 'mv --help' for more information.
| |
| − | (base) [ehspector@login2 gas_teiger]$ mv gas_3.in test
| |
| − | (base) [ehspector@login2 gas_teiger]$ cd test/
| |
| − | (base) [ehspector@login2 test]$ ls
| |
| − | gas_3.in test_nocharge.mol2
| |
| − | (base) [ehspector@login2 test]$ vi test_nocharge.mol2
| |
| − | (base) [ehspector@login2 test]$ vi gas_3.in
| |
| − | (base) [ehspector@login2 test]$ dock6 -i gas_3.in -o gas_3.out
| |
| − | (base) [ehspector@login2 test]$ ls
| |
| − | gas_3.in gas_3.out gas_3.out_scored.mol2 test_nocharge.mol2
| |
| − | (base) [ehspector@login2 test]$ vi gas_3.out
| |
| − | (base) [ehspector@login2 test]$ vi gas_3.out_scored.mol2
| |
| − | (base) [ehspector@login2 test]$ vi gas_3.out
| |
| − | (base) [ehspector@login2 test]$ cd ..
| |
| − | (base) [ehspector@login2 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@login2 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@login2 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.out gas_5.in gas.out_scored.mol2 test
| |
| − | 1AAQ_yesG.mol2 gas_3.out_scored.mol2 gas_5.out no_charge test.mol2
| |
| − | gas_2.in gas_4.in gas_5.out_scored.mol2 no_gas.in
| |
| − | gas_2.out gas_4.out gas.in no_gas.out
| |
| − | gas_2.out_scored.mol2 gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_4.in
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_4.in
| |
| − | (base) [ehspector@login2 gas_teiger]$ dock6 -i gas_4.in -o gas_4.out
| |
| − | (base) [ehspector@login2 gas_teiger]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.out gas_5.in gas.out_scored.mol2 test
| |
| − | 1AAQ_yesG.mol2 gas_3.out_scored.mol2 gas_5.out no_charge test.mol2
| |
| − | gas_2.in gas_4.in gas_5.out_scored.mol2 no_gas.in
| |
| − | gas_2.out gas_4.out gas.in no_gas.out
| |
| − | gas_2.out_scored.mol2 gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ vi gas_4.out_scored.mol2
| |
| − | (base) [ehspector@login2 gas_teiger]$ cd ..
| |
| − | (base) [ehspector@login2 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@login2 gas_teiger]$ mv gas_4.in test
| |
| − | (base) [ehspector@login2 gas_teiger]$ mv 1AAQ_noG.mol2
| |
| − | mv: missing destination file operand after ‘1AAQ_noG.mol2’
| |
| − | Try 'mv --help' for more information.
| |
| − | (base) [ehspector@login2 gas_teiger]$ mv 1AAQ_noG.mol2 test
| |
| − | (base) [ehspector@login2 gas_teiger]$ home
| |
| − | (base) [ehspector@login2 espector]$ rd
| |
| − | srun: error: invalid partition specified: short-40core
| |
| − | srun: error: Unable to allocate resources: Invalid partition name specified
| |
| − | (base) [ehspector@login2 espector]$ exit
| |
| − | logout
| |
| − | Connection to login.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ rd
| |
| − | srun: job 928167 queued and waiting for resources
| |
| − | ^Csrun: Job allocation 928167 has been revoked
| |
| − | srun: Force Terminated job 928167
| |
| − | (base) [ehspector@milan1 ~]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto R 0:23 3 dg[007-008,041]
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:11:38 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan1 ~]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto R 0:30 3 dg[007-008,041]
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:11:45 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan1 ~]$ cd ..
| |
| − | (base) [ehspector@milan1 home]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/1O86/007_virtualscreen/
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ avail
| |
| − | PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
| |
| − | a100 up 8:00:00 1 mix@ a100-02
| |
| − | a100 up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100 up 8:00:00 1 drain* a100-01
| |
| − | a100 up 8:00:00 2 mix a100-[03,05]
| |
| − | a100 up 8:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | a100-large up 8:00:00 1 mix@ a100-02
| |
| − | a100-large up 8:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-large up 8:00:00 1 drain* a100-01
| |
| − | a100-large up 8:00:00 2 mix a100-[03,05]
| |
| − | a100-large up 8:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | a100-long up 2-00:00:00 1 mix@ a100-02
| |
| − | a100-long up 2-00:00:00 2 alloc@ a100-[07,09]
| |
| − | a100-long up 2-00:00:00 1 drain* a100-01
| |
| − | a100-long up 2-00:00:00 2 mix a100-[03,05]
| |
| − | a100-long up 2-00:00:00 5 alloc a100-[04,06,08,10-11]
| |
| − | debug-40core up 1:00:00 6 plnd dn[024-025,054,056-058]
| |
| − | debug-40core up 1:00:00 5 alloc@ dn[026,029,035,038,045]
| |
| − | debug-40core up 1:00:00 2 drain* dn[031,037]
| |
| − | debug-40core up 1:00:00 5 mix dn[004-005,018,051,061]
| |
| − | debug-40core up 1:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
| |
| − | extended-40core up 7-00:00:00 6 plnd dn[024-025,054,056-058]
| |
| − | extended-40core up 7-00:00:00 5 alloc@ dn[026,029,035,038,045]
| |
| − | extended-40core up 7-00:00:00 2 drain* dn[031,037]
| |
| − | extended-40core up 7-00:00:00 5 mix dn[004-005,018,051,061]
| |
| − | extended-40core up 7-00:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
| |
| − | extended-40core-shared up 3-12:00:00 6 plnd dn[024-025,054,056-058]
| |
| − | extended-40core-shared up 3-12:00:00 5 alloc@ dn[026,029,035,038,045]
| |
| − | extended-40core-shared up 3-12:00:00 2 drain* dn[031,037]
| |
| − | extended-40core-shared up 3-12:00:00 5 mix dn[004-005,018,051,061]
| |
| − | extended-40core-shared up 3-12:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
| |
| − | extended-96core up 7-00:00:00 1 mix@ dg040
| |
| − | extended-96core up 7-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | extended-96core up 7-00:00:00 2 mix dg[009,023]
| |
| − | extended-96core up 7-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
| |
| − | extended-96core up 7-00:00:00 3 idle dg[042,046-047]
| |
| − | extended-96core-shared up 3-12:00:00 1 mix@ dg040
| |
| − | extended-96core-shared up 3-12:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | extended-96core-shared up 3-12:00:00 2 mix dg[009,023]
| |
| − | extended-96core-shared up 3-12:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
| |
| − | extended-96core-shared up 3-12:00:00 3 idle dg[042,046-047]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 3 alloc xm[045-047]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 idle xm048
| |
| − | hbm-extended-96core up 7-00:00:00 3 plnd xm[003,006-007]
| |
| − | hbm-extended-96core up 7-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-extended-96core up 7-00:00:00 1 drain xm017
| |
| − | hbm-extended-96core up 7-00:00:00 76 alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-large-96core up 8:00:00 3 plnd xm[003,006-007]
| |
| − | hbm-large-96core up 8:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-large-96core up 8:00:00 1 drain xm017
| |
| − | hbm-large-96core up 8:00:00 76 alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-long-96core up 2-00:00:00 3 plnd xm[003,006-007]
| |
| − | hbm-long-96core up 2-00:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-long-96core up 2-00:00:00 1 drain xm017
| |
| − | hbm-long-96core up 2-00:00:00 76 alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-medium-96core up 12:00:00 3 plnd xm[003,006-007]
| |
| − | hbm-medium-96core up 12:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-medium-96core up 12:00:00 1 drain xm017
| |
| − | hbm-medium-96core up 12:00:00 76 alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | hbm-short-96core up 4:00:00 3 plnd xm[003,006-007]
| |
| − | hbm-short-96core up 4:00:00 10 alloc@ xm[004-005,013,015,032,039,041,044,049,051]
| |
| − | hbm-short-96core up 4:00:00 1 drain xm017
| |
| − | hbm-short-96core up 4:00:00 76 alloc xm[001-002,008-012,014,016,018-031,033-038,040,042-043,050,052-094]
| |
| − | large-40core up 8:00:00 6 plnd dn[024-025,054,056-058]
| |
| − | large-40core up 8:00:00 5 alloc@ dn[026,029,035,038,045]
| |
| − | large-40core up 8:00:00 2 drain* dn[031,037]
| |
| − | large-40core up 8:00:00 5 mix dn[004-005,018,051,061]
| |
| − | large-40core up 8:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
| |
| − | large-96core up 8:00:00 1 mix@ dg040
| |
| − | large-96core up 8:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | large-96core up 8:00:00 2 mix dg[009,023]
| |
| − | large-96core up 8:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
| |
| − | large-96core up 8:00:00 3 idle dg[042,046-047]
| |
| − | long-40core up 2-00:00:00 6 plnd dn[024-025,054,056-058]
| |
| − | long-40core up 2-00:00:00 5 alloc@ dn[026,029,035,038,045]
| |
| − | long-40core up 2-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core up 2-00:00:00 5 mix dn[004-005,018,051,061]
| |
| − | long-40core up 2-00:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
| |
| − | long-40core-shared up 1-00:00:00 6 plnd dn[024-025,054,056-058]
| |
| − | long-40core-shared up 1-00:00:00 5 alloc@ dn[026,029,035,038,045]
| |
| − | long-40core-shared up 1-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core-shared up 1-00:00:00 5 mix dn[004-005,018,051,061]
| |
| − | long-40core-shared up 1-00:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
| |
| − | long-96core up 2-00:00:00 1 mix@ dg040
| |
| − | long-96core up 2-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | long-96core up 2-00:00:00 2 mix dg[009,023]
| |
| − | long-96core up 2-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
| |
| − | long-96core up 2-00:00:00 3 idle dg[042,046-047]
| |
| − | long-96core-shared up 1-00:00:00 1 mix@ dg040
| |
| − | long-96core-shared up 1-00:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | long-96core-shared up 1-00:00:00 2 mix dg[009,023]
| |
| − | long-96core-shared up 1-00:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
| |
| − | long-96core-shared up 1-00:00:00 3 idle dg[042,046-047]
| |
| − | medium-40core up 12:00:00 6 plnd dn[024-025,054,056-058]
| |
| − | medium-40core up 12:00:00 5 alloc@ dn[026,029,035,038,045]
| |
| − | medium-40core up 12:00:00 2 drain* dn[031,037]
| |
| − | medium-40core up 12:00:00 5 mix dn[004-005,018,051,061]
| |
| − | medium-40core up 12:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
| |
| − | medium-96core up 12:00:00 1 mix@ dg040
| |
| − | medium-96core up 12:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | medium-96core up 12:00:00 2 mix dg[009,023]
| |
| − | medium-96core up 12:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
| |
| − | medium-96core up 12:00:00 3 idle dg[042,046-047]
| |
| − | ood-short-96core up 4:00:00 1 idle dg038
| |
| − | rn-long-40core up 8-08:00:00 12 idle rn[001-012]
| |
| − | short-40core up 4:00:00 6 plnd dn[024-025,054,056-058]
| |
| − | short-40core up 4:00:00 5 alloc@ dn[026,029,035,038,045]
| |
| − | short-40core up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core up 4:00:00 5 mix dn[004-005,018,051,061]
| |
| − | short-40core up 4:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
| |
| − | short-40core-shared up 4:00:00 6 plnd dn[024-025,054,056-058]
| |
| − | short-40core-shared up 4:00:00 5 alloc@ dn[026,029,035,038,045]
| |
| − | short-40core-shared up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core-shared up 4:00:00 5 mix dn[004-005,018,051,061]
| |
| − | short-40core-shared up 4:00:00 44 alloc dn[001-003,006-017,019-023,027-028,030,032-034,036,039-044,046-050,052-053,055,059-060,062]
| |
| − | short-96core up 4:00:00 1 mix@ dg040
| |
| − | short-96core up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | short-96core up 4:00:00 2 mix dg[009,023]
| |
| − | short-96core up 4:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
| |
| − | short-96core up 4:00:00 3 idle dg[042,046-047]
| |
| − | short-96core-shared up 4:00:00 1 mix@ dg040
| |
| − | short-96core-shared up 4:00:00 7 alloc@ dg[013,024,028-029,033-034,043]
| |
| − | short-96core-shared up 4:00:00 2 mix dg[009,023]
| |
| − | short-96core-shared up 4:00:00 34 alloc dg[001-008,010-012,014-022,025-027,030-032,035-037,039,041,044-045,048]
| |
| − | short-96core-shared up 4:00:00 3 idle dg[042,046-047]
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ vi virtual.in
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ sbatch virtual.sh
| |
| − | Submitted batch job 928174
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928174 ood-short 1O86_vs_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto R 3:06 3 dg[007-008,041]
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:14:21 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928174 ood-short 1O86_vs_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto R 3:49 3 dg[007-008,041]
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:15:04 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928174 ood-short 1O86_vs_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto R 3:52 3 dg[007-008,041]
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:15:07 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ sbatch virtual.sh
| |
| − | Submitted batch job 928179
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928174 ood-short 1O86_vs_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928179 short-96c 1O86_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | 928070 short-96c 5een_vs_ ehspecto R 4:21 3 dg[007-008,041]
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:15:36 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928174 ood-short 1O86_vs_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928179 short-96c 1O86_vs_ ehspecto PD 0:00 3 (Priority)
| |
| − | 928070 short-96c 5een_vs_ ehspecto R 4:22 3 dg[007-008,041]
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:15:37 3 dg[032,035-036]
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928174 ood-short 1O86_vs_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto R 4:55 3 dg[007-008,041]
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:16:10 3 dg[032,035-036]
| |
| − | 928179 short-96c 1O86_vs_ ehspecto R 0:24 3 dg[026,046-047]
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928174 ood-short 1O86_vs_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto R 5:47 3 dg[007-008,041]
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:17:02 3 dg[032,035-036]
| |
| − | 928179 short-96c 1O86_vs_ ehspecto R 1:16 3 dg[026,046-047]
| |
| − | (base) [ehspector@milan1 007_virtualscreen]$ home
| |
| − | (base) [ehspector@milan1 espector]$ rd
| |
| − | srun: job 928192 queued and waiting for resources
| |
| − | srun: job 928192 has been allocated resources
| |
| − | (base) [ehspector@dn050 espector]$ cd builds/alpha_branch/install/
| |
| − | (base) [ehspector@dn050 install]$ ls
| |
| − | bluegenel docker gnu.parallel homebrew intel.intelmpi.parallel Makefile sgi
| |
| − | bluegenep gnu gnu.parallel.rdkit homebrew.rdkit intel.ip.mkl oneapi sgi.parallel
| |
| − | config.h gnu.acml gnu.rdkit ibmaix intel.mkl pgi test
| |
| − | configure gnu.gdb gnu.valgrind intel intel.parallel rules.h
| |
| − | (base) [ehspector@dn050 install]$ configure gnu.rdkit
| |
| − | bash: configure: command not found
| |
| − | (base) [ehspector@dn050 install]$ ./configure gnu.rdkit
| |
| − | The requested configuration file was found.
| |
| − |
| |
| − | Warning: the configuration file already exists with the creation stamp:
| |
| − | # Created at Wed Feb 12 10:29:31 EST 2025 via ./configure gnu
| |
| − | It will be overwritten !
| |
| − |
| |
| − | Don't forget to make clean before rebuilding.
| |
| − | To reconfigure and rebuild everything start with make -i distclean:
| |
| − | Reconfiguring after make -i distclean will avoid this warning.
| |
| − |
| |
| − | The DOCK configuration file has been created.
| |
| − | REQUIREMENTS - define these environment variables
| |
| − | RDBASE is the root directory of RDKit
| |
| − | BOOST is the root directory of Boost
| |
| − | (base) [ehspector@dn050 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn050 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Thu Feb 13 11:55:37 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from filter.h:10,
| |
| − | from filter.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from filter.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fingerprint.h:13,
| |
| − | from fingerprint.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from fingerprint.h:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fraggraph.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fraggraph.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fragment.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fragment.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from gasteiger.h:8,
| |
| − | from gasteiger.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from gasteiger.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from hungarian.h:7,
| |
| − | from hungarian.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from hungarian.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from library_file.h:9,
| |
| − | from library_file.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from library_file.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o limit_max_change.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from limit_max_change.h:12,
| |
| − | from limit_max_change.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from limit_max_change.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o master_conf.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from master_conf.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from master_conf.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o master_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from master_score.h:5,
| |
| − | from master_score.cpp:2:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from master_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o orient.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from orient.h:7,
| |
| − | from orient.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from orient.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o sasa.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from sasa.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from sasa.h:14:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o score_amber.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_amber.cpp:66:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
| |
| − | from score_amber.cpp:55:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o score_chemgrid.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_chemgrid.cpp:39:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
| |
| − | from score_chemgrid.cpp:38:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o score_descriptor.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_descriptor.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_descriptor.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o score_footprint.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_footprint.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_footprint.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o score_ph4.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_ph4.h:7,
| |
| − | from score_ph4.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_ph4.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o score_volume.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_volume.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_volume.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o score_gist.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_gist.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_gist.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o score_hbond.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_hbond.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_hbond.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o score_internal.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_internal.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_internal.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o score_multigrid.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_multigrid.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_multigrid.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o score_sasa.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from score_sasa.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_sasa.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o score_solvent.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from score_solvent.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_solvent.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o simplex.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from master_score.h:5,
| |
| − | from simplex.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from simplex.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o sphere.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o trace.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o utils.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from utils.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from utils.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o iso_align.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fragment.h:12,
| |
| − | from iso_align.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from fragment.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o mem_info.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o rdtyper.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
| |
| − | from rdtyper.cpp:18:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from rdtyper.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o rddrive.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from rddrive.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from dockmol.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | cd nab && make all
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | gcc -c -O3 -D_ANSI_SOURCE molio.c
| |
| − | gcc -c -O2 -o prm.o prm.c
| |
| − | make is_LEX_available
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c
| |
| − | gcc -c -O2 -o traceback.o traceback.c
| |
| − | gcc -c -O2 -o select_atoms.o select_atoms.c
| |
| − | gcc -c -O2 -o memutil.o memutil.c
| |
| − | gcc -c -O2 -o reslib.o reslib.c
| |
| − | gcc -c -O2 -o jacobi.o jacobi.c
| |
| − | gcc -c -O2 -o molutil.o molutil.c
| |
| − | gcc -c -O2 -o chirvol.o chirvol.c
| |
| − | gcc -c -O2 -o regexp.o regexp.c
| |
| − | gcc -c -O2 -o binpos.o binpos.c
| |
| − | gcc -c -O2 -o time.o time.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE rand2.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE conjgrad.c
| |
| − | gcc -c -O2 -o database.o database.c
| |
| − | gcc -c -O2 -o tleap.o tleap.c
| |
| − | ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
| |
| − | ar: creating nab.a
| |
| − | a - molio.o
| |
| − | a - prm.o
| |
| − | a - sff.o
| |
| − | a - traceback.o
| |
| − | a - select_atoms.o
| |
| − | a - memutil.o
| |
| − | a - reslib.o
| |
| − | a - jacobi.o
| |
| − | a - molutil.o
| |
| − | a - chirvol.o
| |
| − | a - regexp.o
| |
| − | a - binpos.o
| |
| − | a - time.o
| |
| − | a - rand2.o
| |
| − | a - conjgrad.o
| |
| − | a - database.o
| |
| − | a - tleap.o
| |
| − | ranlib nab.a
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
| |
| − | ar cr libgzstream.a gzstream.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
| |
| − | -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
| |
| − | mv dock6.rdkit ../../bin
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − |
| |
| − | Installation of
| |
| − | DOCK v6.12
| |
| − | program dock is complete at Thu Feb 13 11:58:47 EST 2025.
| |
| − |
| |
| − | (base) [ehspector@dn050 install]$ cd ..
| |
| − | (base) [ehspector@dn050 alpha_branch]$ exit
| |
| − | exit
| |
| − | (base) [ehspector@milan1 espector]$ cd 4s0v/gas_teiger/test/
| |
| − | (base) [ehspector@milan1 test]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.in gas_3.out gas_3.out_scored.mol2 gas_4.in test_nocharge.mol2
| |
| − | (base) [ehspector@milan1 test]$ vi gas_4.in
| |
| − | (base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out
| |
| − | (base) [ehspector@milan1 test]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.in gas_3.out gas_3.out_scored.mol2 gas_4.in gas_4.out test_nocharge.mol2
| |
| − | (base) [ehspector@milan1 test]$ vi gas_4.out
| |
| − | (base) [ehspector@milan1 test]$ vi gas_4.in
| |
| − | (base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out
| |
| − | (base) [ehspector@milan1 test]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.out gas_4.in gas_4.out_scored.mol2
| |
| − | gas_3.in gas_3.out_scored.mol2 gas_4.out test_nocharge.mol2
| |
| − | (base) [ehspector@milan1 test]$ vi gas_4.out
| |
| − | (base) [ehspector@milan1 test]$ vi gas_4.in
| |
| − | (base) [ehspector@milan1 test]$ dock6 -i gas_4.in -o gas_4.out
| |
| − | (base) [ehspector@milan1 test]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.out gas_4.in gas_4.out_scored.mol2
| |
| − | gas_3.in gas_3.out_scored.mol2 gas_4.out test_nocharge.mol2
| |
| − | (base) [ehspector@milan1 test]$ vi gas_4.out
| |
| − | (base) [ehspector@milan1 test]$ vi gas_4.out_scored.mol2
| |
| − | (base) [ehspector@milan1 test]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928174 ood-short 1O86_vs_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 928060 short-40c 5een_vs_ ehspecto PD 0:00 4 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)
| |
| − | 928070 short-96c 5een_vs_ ehspecto R 16:05 3 dg[007-008,041]
| |
| − | 928053 short-96c 2w26_vs_ ehspecto R 1:27:20 3 dg[032,035-036]
| |
| − | 928179 short-96c 1O86_vs_ ehspecto R 11:34 3 dg[026,046-047]
| |
| − | (base) [ehspector@milan1 test]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 928174 ood-short 1O86_vs_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | (base) [ehspector@milan2 ~]$ scancel 928174
| |
| − | (base) [ehspector@milan2 ~]$ ls
| |
| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@milan2 ~]$ cd AMS_536/
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/007_virtual_screen/
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ ls
| |
| − | virtual.in virtual.out virtual_scored.mol2 virtual.sh vs_output.txt
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ grep -c "Name" virtual_scored.mol2
| |
| − | 97
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 5EEN/007_virtualscreen/
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ ls
| |
| − | virtual.in virtual.out virtual_scored.mol2 virtual.sh vs_output.txt
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ grep -c "Name" virtual_scored.mol2
| |
| − | 97
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ cd ../../1O86/007_virtualscreen/
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ ls
| |
| − | virtual.in virtual.out virtual_scored.mol2 virtual.sh vs_output.txt
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ grep -c "Name" virtual_scored.mol2
| |
| − | 97
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ cd ../../
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/006_footprint/
| |
| − | (base) [ehspector@milan2 006_footprint]$ pwd
| |
| − | /gpfs/home/ehspector/AMS_536/Tutorials/2w26/006_footprint
| |
| − | (base) [ehspector@milan2 006_footprint]$ cd ../
| |
| − | (base) [ehspector@milan2 2w26]$ cd 007_virtual_screen/
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ ls
| |
| − | virtual.in virtual.out virtual_scored.mol2 virtual.sh vs_output.txt
| |
| − | (base) [ehspector@milan2 007_virtual_screen]$ cd ../../5EEN/
| |
| − | (base) [ehspector@milan2 5EEN]$ cd 007_virtualscreen/
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ cd ../
| |
| − | (base) [ehspector@milan2 5EEN]$ cd ../
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/
| |
| − | (base) [ehspector@milan2 1O86]$ cd 007_virtualscreen/
| |
| − | (base) [ehspector@milan2 007_virtualscreen]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
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| − | ehspector@milan.seawulf.stonybrook.edu's password:
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| − | Duo two-factor login for ehspector
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| − |
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| − | Enter a passcode or select one of the following options:
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| − |
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| − | 1. Duo Push to XXX-XXX-9204
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| − |
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| − | Passcode or option (1-1): 1
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| − |
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| − | Pushed a login request to your device...
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| − | Success. Logging you in...
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| − | Loading gcc-stack
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| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
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| − | (base) [ehspector@milan2 ~]$ ls
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| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
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| − | (base) [ehspector@milan2 ~]$ cd AMS_536/
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| − | (base) [ehspector@milan2 AMS_536]$ ls
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| − | class_project commands.txt Notes.txt Tutorials
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| − | (base) [ehspector@milan2 AMS_536]$ home
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| − | (base) [ehspector@milan2 espector]$ cd builds/alpha_branch/src/dock
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| − | (base) [ehspector@milan2 dock]$ ls
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| − | amber_typer.cpp filter.o mem_info.h score_internal.cpp
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| − | amber_typer.h fingerprint.cpp mem_info.o score_internal.h
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| − | amber_typer.o fingerprint.h nab score_internal.o
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| − | base_grid.cpp fingerprint.o nabcode.h score_multigrid.cpp
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| − | base_grid.h fraggraph.cpp nab.h score_multigrid.h
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| − | base_grid.o fraggraph.h orient.cpp score_multigrid.o
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| − | base_mpi.cpp fraggraph.o orient.h score.o
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| − | base_mpi.h fragment.cpp orient.o score_ph4.cpp
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| − | base_mpi.o fragment.h rddrive.cpp score_ph4.h
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| − | base_score.cpp fragment.o rddrive.h score_ph4.o
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| − | base_score.h gasteiger.cpp rddrive.o score_sasa.cpp
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| − | base_score.o gasteiger.h rdtyper.cpp score_sasa.h
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| − | conf_gen_ag.cpp gasteiger.o rdtyper.h score_sasa.o
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| − | conf_gen_ag.h grid.cpp rdtyper.o score_solvent.cpp
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| − | conf_gen_ag.o grid.h README score_solvent.h
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| − | conf_gen_cg.cpp grid.o sasa.cpp score_solvent.o
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| − | conf_gen_cg.h gzstream sasa.h score_volume.cpp
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| − | conf_gen_cg.o hungarian.cpp sasa.o score_volume.h
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| − | conf_gen_dn.cpp hungarian.h score_amber.cpp score_volume.o
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| − | conf_gen_dn_ga.cpp hungarian.o score_amber.h simplex.cpp
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| − | conf_gen_dn_ga.h iso_align.cpp score_amber.o simplex.h
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| − | conf_gen_dn_ga.o iso_align.h score_chemgrid.cpp simplex.o
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| − | conf_gen_dn.h iso_align.o score_chemgrid.h sphere.cpp
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| − | conf_gen_dn.o library_file.cpp score_chemgrid.o sphere.h
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| − | conf_gen_ga.cpp library_file.h score.cpp sphere.o
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| − | conf_gen_ga.h library_file.o score_descriptor.cpp tnt
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| − | conf_gen_ga.o limit_max_change.cpp score_descriptor.h trace.cpp
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| − | conf_gen_hdb.cpp limit_max_change.h score_descriptor.o trace.h
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| − | conf_gen_hdb.h limit_max_change.o score_footprint.cpp trace.inl
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| − | conf_gen_hdb.o lol score_footprint.h trace.o
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| − | defreal.h Makefile score_footprint.o utils.cpp
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| − | dock.cpp master_conf.cpp score_gist.cpp utils.h
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| − | dockmol.cpp master_conf.h score_gist.h utils.o
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| − | dockmol.h master_conf.o score_gist.o version.h
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| − | dockmol.o master_score.cpp score.h xlogp.cpp
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| − | dock.o master_score.h score_hbond.cpp xlogp.h
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| − | filter.cpp master_score.o score_hbond.h
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| − | filter.h mem_info.cpp score_hbond.o
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| − | (base) [ehspector@milan2 dock]$ ls
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| − | amber_typer.cpp filter.o mem_info.h score_internal.cpp
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| − | amber_typer.h fingerprint.cpp mem_info.o score_internal.h
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| − | amber_typer.o fingerprint.h nab score_internal.o
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| − | base_grid.cpp fingerprint.o nabcode.h score_multigrid.cpp
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| − | base_grid.h fraggraph.cpp nab.h score_multigrid.h
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| − | base_grid.o fraggraph.h orient.cpp score_multigrid.o
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| − | base_mpi.cpp fraggraph.o orient.h score.o
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| − | base_mpi.h fragment.cpp orient.o score_ph4.cpp
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| − | base_mpi.o fragment.h rddrive.cpp score_ph4.h
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| − | base_score.cpp fragment.o rddrive.h score_ph4.o
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| − | base_score.h gasteiger.cpp rddrive.o score_sasa.cpp
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| − | base_score.o gasteiger.h rdtyper.cpp score_sasa.h
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| − | conf_gen_ag.cpp gasteiger.o rdtyper.h score_sasa.o
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| − | conf_gen_ag.h grid.cpp rdtyper.o score_solvent.cpp
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| − | conf_gen_ag.o grid.h README score_solvent.h
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| − | conf_gen_cg.cpp grid.o sasa.cpp score_solvent.o
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| − | conf_gen_cg.h gzstream sasa.h score_volume.cpp
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| − | conf_gen_cg.o hungarian.cpp sasa.o score_volume.h
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| − | conf_gen_dn.cpp hungarian.h score_amber.cpp score_volume.o
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| − | conf_gen_dn_ga.cpp hungarian.o score_amber.h simplex.cpp
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| − | conf_gen_dn_ga.h iso_align.cpp score_amber.o simplex.h
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| − | conf_gen_dn_ga.o iso_align.h score_chemgrid.cpp simplex.o
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| − | conf_gen_dn.h iso_align.o score_chemgrid.h sphere.cpp
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| − | conf_gen_dn.o library_file.cpp score_chemgrid.o sphere.h
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| − | conf_gen_ga.cpp library_file.h score.cpp sphere.o
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| − | conf_gen_ga.h library_file.o score_descriptor.cpp tnt
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| − | conf_gen_ga.o limit_max_change.cpp score_descriptor.h trace.cpp
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| − | conf_gen_hdb.cpp limit_max_change.h score_descriptor.o trace.h
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| − | conf_gen_hdb.h limit_max_change.o score_footprint.cpp trace.inl
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| − | conf_gen_hdb.o lol score_footprint.h trace.o
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| − | defreal.h Makefile score_footprint.o utils.cpp
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| − | dock.cpp master_conf.cpp score_gist.cpp utils.h
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| − | dockmol.cpp master_conf.h score_gist.h utils.o
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| − | dockmol.h master_conf.o score_gist.o version.h
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| − | dockmol.o master_score.cpp score.h xlogp.cpp
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| − | dock.o master_score.h score_hbond.cpp xlogp.h
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| − | filter.cpp master_score.o score_hbond.h
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| − | filter.h mem_info.cpp score_hbond.o
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| − | (base) [ehspector@milan2 dock]$ grep parameters
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| − | ^C
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| − | (base) [ehspector@milan2 dock]$ grep -c "parameters"
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| − | ^C
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| − | (base) [ehspector@milan2 dock]$ grep -c "parameters" library_file.cpp
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| − | 3
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| − | (base) [ehspector@milan2 dock]$ vi library_file.cpp
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| − | (base) [ehspector@milan2 dock]$ vi filter.cpp
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| − | (base) [ehspector@milan2 dock]$ vi filter.cpp
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| − | (base) [ehspector@milan2 dock]$ vi dockmol.cpp
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| − | (base) [ehspector@milan2 dock]$ rd
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| − | srun: job 931653 queued and waiting for resources
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| − | srun: job 931653 has been allocated resources
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| − | (base) [ehspector@dn033 dock]$ cd ../../install/
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| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
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| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
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| − | make -C dock clean
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| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
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| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
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| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
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| − | /bin/rm -f *.o nab.a lex.mm_options.c
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| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
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| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
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| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
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| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
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| − | make -C accessories clean
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| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
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| − | /bin/rm -f showbox.o showsphere.o sphgen.o
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
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| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
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| − | make -C schemgrid_GB clean
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| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
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| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
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| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
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| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
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| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
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| − | make -C grid clean
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| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
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| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
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| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
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| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
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| − | make -C antechamber clean
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| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
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| − | /bin/rm -f *.o
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
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| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 16:28:08 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:917:16: error: ‘class Filter’ has no member named ‘mol_status’
| |
| − | 917 | if (filter.mol_status = false){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ cd ../../
| |
| − | (base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 16:30:26 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
| |
| − | 917 | if (filter.gasteigerize.mol_status = false){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ cd ../../
| |
| − | (base) [ehspector@dn033 builds]$ ls
| |
| − | alpha_branch dock6-master dock6-master.zip dock6-rdkit
| |
| − | (base) [ehspector@dn033 builds]$ cd alpha_branch/src/
| |
| − | (base) [ehspector@dn033 src]$ ls
| |
| − | accessories dock gbsa_grids Makefile rdkit tleap
| |
| − | antechamber docktools grid mopac6 resp
| |
| − | (base) [ehspector@dn033 src]$ ls
| |
| − | accessories dock gbsa_grids Makefile rdkit tleap
| |
| − | antechamber docktools grid mopac6 resp
| |
| − | (base) [ehspector@dn033 src]$ cd dock
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 16:33:59 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
| |
| − | 917 | if (filter.gasteigerize.mol_status = no){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | dockmol.cpp:917:42: error: ‘no’ was not declared in this scope; did you mean ‘boost::concepts::detail::no’?
| |
| − | 917 | if (filter.gasteigerize.mol_status = no){
| |
| − | | ^~
| |
| − | | boost::concepts::detail::no
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/general.hpp:12,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/assert.hpp:35,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/property_map/property_map.hpp:19,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:28:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/has_constraints.hpp:19:18: note: ‘boost::concepts::detail::no’ declared here
| |
| − | 19 | typedef char (&no)[2];
| |
| − | | ^~
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ cd ../../
| |
| − | (base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
| |
| − | (base) [ehspector@dn033 dock]$ ls
| |
| − | amber_typer.cpp conf_gen_hdb.o master_conf.cpp score.h
| |
| − | amber_typer.h defreal.h master_conf.h score_hbond.cpp
| |
| − | amber_typer.o dock.cpp master_score.cpp score_hbond.h
| |
| − | base_grid.cpp dockmol.cpp master_score.h score_internal.cpp
| |
| − | base_grid.h dockmol.h mem_info.cpp score_internal.h
| |
| − | base_grid.o dock.o mem_info.h score_multigrid.cpp
| |
| − | base_mpi.cpp filter.cpp nab score_multigrid.h
| |
| − | base_mpi.h filter.h nabcode.h score_ph4.cpp
| |
| − | base_mpi.o fingerprint.cpp nab.h score_ph4.h
| |
| − | base_score.cpp fingerprint.h orient.cpp score_sasa.cpp
| |
| − | base_score.h fraggraph.cpp orient.h score_sasa.h
| |
| − | base_score.o fraggraph.h rddrive.cpp score_solvent.cpp
| |
| − | conf_gen_ag.cpp fragment.cpp rddrive.h score_solvent.h
| |
| − | conf_gen_ag.h fragment.h rdtyper.cpp score_volume.cpp
| |
| − | conf_gen_ag.o gasteiger.cpp rdtyper.h score_volume.h
| |
| − | conf_gen_cg.cpp gasteiger.h README simplex.cpp
| |
| − | conf_gen_cg.h grid.cpp sasa.cpp simplex.h
| |
| − | conf_gen_cg.o grid.h sasa.h sphere.cpp
| |
| − | conf_gen_dn.cpp gzstream score_amber.cpp sphere.h
| |
| − | conf_gen_dn_ga.cpp hungarian.cpp score_amber.h tnt
| |
| − | conf_gen_dn_ga.h hungarian.h score_chemgrid.cpp trace.cpp
| |
| − | conf_gen_dn_ga.o iso_align.cpp score_chemgrid.h trace.h
| |
| − | conf_gen_dn.h iso_align.h score.cpp trace.inl
| |
| − | conf_gen_dn.o library_file.cpp score_descriptor.cpp utils.cpp
| |
| − | conf_gen_ga.cpp library_file.h score_descriptor.h utils.h
| |
| − | conf_gen_ga.h limit_max_change.cpp score_footprint.cpp version.h
| |
| − | conf_gen_ga.o limit_max_change.h score_footprint.h xlogp.cpp
| |
| − | conf_gen_hdb.cpp lol score_gist.cpp xlogp.h
| |
| − | conf_gen_hdb.h Makefile score_gist.h
| |
| − | (base) [ehspector@dn033 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@dn033 dock]$ vi filter.h
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ../../
| |
| − | (base) [ehspector@dn033 alpha_branch]$ ls
| |
| − | bin docs parameters README.md template_pipeline
| |
| − | developer install README src tutorials
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd src/
| |
| − | (base) [ehspector@dn033 src]$ cd ../
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 16:45:39 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
| |
| − | 917 | if (filter.gasteigerize.mol_status = false){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ cd ../
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd src/
| |
| − | (base) [ehspector@dn033 src]$ ls
| |
| − | accessories dock gbsa_grids Makefile rdkit tleap
| |
| − | antechamber docktools grid mopac6 resp
| |
| − | (base) [ehspector@dn033 src]$ cd dock
| |
| − | (base) [ehspector@dn033 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ../
| |
| − | (base) [ehspector@dn033 src]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 src]$ cd dock
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ../../
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 16:52:20 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
| |
| − | 917 | if (filter.gasteigerize.mol_status = false){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ cd ..
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd src/dock
| |
| − | (base) [ehspector@dn033 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ..
| |
| − | (base) [ehspector@dn033 src]$ cd ../
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@dn033 install]$ ls
| |
| − | bluegenel gnu.acml homebrew intel.mkl sgi
| |
| − | bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel
| |
| − | config.h gnu.parallel ibmaix Makefile test
| |
| − | configure gnu.parallel.rdkit intel oneapi
| |
| − | docker gnu.rdkit intel.intelmpi.parallel pgi
| |
| − | gnu gnu.valgrind intel.ip.mkl rules.h
| |
| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
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| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
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| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
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| − | make -C tleap clean
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| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
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| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
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| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
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| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
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| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
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| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
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| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
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| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 16:55:45 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | dockmol.cpp:917:43: warning: multi-character character constant [-Wmultichar]
| |
| − | 917 | if (filter.gasteigerize.mol_status == 'no'){
| |
| − | | ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
| |
| − | 917 | if (filter.gasteigerize.mol_status == 'no'){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ cd ..
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd src/dock
| |
| − | (base) [ehspector@dn033 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
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| − | make -C resp clean
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| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
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| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
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| − | make -C docktools clean
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| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
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| − | make -C chemgrids clean
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| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
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| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
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| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
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| − | make -C solvgrids clean
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| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
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| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
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| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
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| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
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| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
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| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
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| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
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| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 16:58:13 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:917:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
| |
| − | 917 | if (filter.gasteigerize.mol_status = false){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ cd ../../
| |
| − | (base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
| |
| − | (base) [ehspector@dn033 dock]$ vi library_file.cpp
| |
| − | (base) [ehspector@dn033 dock]$ vi library_file.h
| |
| − | (base) [ehspector@dn033 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ../../
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
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| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
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| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
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| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 17:06:34 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:917:29: error: ‘mol_status’ was not declared in this scope
| |
| − | 917 | if (filter.gasteigerize(mol_status) = false){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | dockmol.cpp:917:39: error: expression cannot be used as a function
| |
| − | 917 | if (filter.gasteigerize(mol_status) = false){
| |
| − | | ^
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ vi filter.cpp
| |
| − | (base) [ehspector@dn033 install]$ cd ../../
| |
| − | (base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
| |
| − | (base) [ehspector@dn033 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@dn033 dock]$ vi filter.h
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ..
| |
| − | (base) [ehspector@dn033 src]$ cd ../
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 17:16:17 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:917:30: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
| |
| − | 917 | if (!filter.gasteigerize.mol_status){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ cd ../
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd src/dock
| |
| − | (base) [ehspector@dn033 dock]$ vi library_file.cpp
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ../../
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 17:59:26 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:780:5: error: ‘mol_status’ was not declared in this scope
| |
| − | 780 | mol_status = false;
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
| |
| − | 919 | if (filter.gasteigerize.mol_status){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 install]$ cd ../
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd ../
| |
| − | (base) [ehspector@dn033 builds]$ cd ../
| |
| − | (base) [ehspector@dn033 espector]$ cd builds/alpha_branch/src/dock
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ..
| |
| − | (base) [ehspector@dn033 src]$ cd ../
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 18:02:33 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
| |
| − | 919 | if (filter.gasteigerize.mol_status = false){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ cd ../../
| |
| − | (base) [ehspector@dn033 builds]$ cd alpha_branch/src/
| |
| − | (base) [ehspector@dn033 src]$ ;s
| |
| − | bash: syntax error near unexpected token `;'
| |
| − | (base) [ehspector@dn033 src]$ ls
| |
| − | accessories dock gbsa_grids Makefile rdkit tleap
| |
| − | antechamber docktools grid mopac6 resp
| |
| − | (base) [ehspector@dn033 src]$ cd dock
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 18:06:37 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:919:16: error: ‘gasteigerize’ is not a class, namespace, or enumeration
| |
| − | 919 | if (filter.gasteigerize::mol_status = no){
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~
| |
| − | dockmol.cpp:919:43: error: ‘no’ was not declared in this scope; did you mean ‘boost::concepts::detail::no’?
| |
| − | 919 | if (filter.gasteigerize::mol_status = no){
| |
| − | | ^~
| |
| − | | boost::concepts::detail::no
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/general.hpp:12,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/assert.hpp:35,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/property_map/property_map.hpp:19,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:28:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/concept/detail/has_constraints.hpp:19:18: note: ‘boost::concepts::detail::no’ declared here
| |
| − | 19 | typedef char (&no)[2];
| |
| − | | ^~
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 install]$ cd ..
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@dn033 install]$ ls
| |
| − | bluegenel gnu.acml homebrew intel.mkl sgi
| |
| − | bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel
| |
| − | config.h gnu.parallel ibmaix Makefile test
| |
| − | configure gnu.parallel.rdkit intel oneapi
| |
| − | docker gnu.rdkit intel.intelmpi.parallel pgi
| |
| − | gnu gnu.valgrind intel.ip.mkl rules.h
| |
| − | (base) [ehspector@dn033 install]$ cd ../../
| |
| − | (base) [ehspector@dn033 builds]$ cd ..
| |
| − | (base) [ehspector@dn033 espector]$ cd builds/alpha_branch/src/dock
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn033 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 18:11:54 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:919:16: error: ‘class Filter’ has no member named ‘mol_status’
| |
| − | 919 | if (filter.mol_status = false){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ cd ..
| |
| − | (base) [ehspector@dn033 alpha_branch]$ cd ..
| |
| − | (base) [ehspector@dn033 builds]$ cd alpha_branch/src/
| |
| − | (base) [ehspector@dn033 src]$ ;s
| |
| − | bash: syntax error near unexpected token `;'
| |
| − | (base) [ehspector@dn033 src]$ ls
| |
| − | accessories dock gbsa_grids Makefile rdkit tleap
| |
| − | antechamber docktools grid mopac6 resp
| |
| − | (base) [ehspector@dn033 src]$ cd dock
| |
| − | (base) [ehspector@dn033 dock]$ ls
| |
| − | amber_typer.cpp conf_gen_hdb.o master_conf.cpp score.h
| |
| − | amber_typer.h defreal.h master_conf.h score_hbond.cpp
| |
| − | amber_typer.o dock.cpp master_score.cpp score_hbond.h
| |
| − | base_grid.cpp dockmol.cpp master_score.h score_internal.cpp
| |
| − | base_grid.h dockmol.h mem_info.cpp score_internal.h
| |
| − | base_grid.o dock.o mem_info.h score_multigrid.cpp
| |
| − | base_mpi.cpp filter.cpp nab score_multigrid.h
| |
| − | base_mpi.h filter.h nabcode.h score_ph4.cpp
| |
| − | base_mpi.o fingerprint.cpp nab.h score_ph4.h
| |
| − | base_score.cpp fingerprint.h orient.cpp score_sasa.cpp
| |
| − | base_score.h fraggraph.cpp orient.h score_sasa.h
| |
| − | base_score.o fraggraph.h rddrive.cpp score_solvent.cpp
| |
| − | conf_gen_ag.cpp fragment.cpp rddrive.h score_solvent.h
| |
| − | conf_gen_ag.h fragment.h rdtyper.cpp score_volume.cpp
| |
| − | conf_gen_ag.o gasteiger.cpp rdtyper.h score_volume.h
| |
| − | conf_gen_cg.cpp gasteiger.h README simplex.cpp
| |
| − | conf_gen_cg.h grid.cpp sasa.cpp simplex.h
| |
| − | conf_gen_cg.o grid.h sasa.h sphere.cpp
| |
| − | conf_gen_dn.cpp gzstream score_amber.cpp sphere.h
| |
| − | conf_gen_dn_ga.cpp hungarian.cpp score_amber.h tnt
| |
| − | conf_gen_dn_ga.h hungarian.h score_chemgrid.cpp trace.cpp
| |
| − | conf_gen_dn_ga.o iso_align.cpp score_chemgrid.h trace.h
| |
| − | conf_gen_dn.h iso_align.h score.cpp trace.inl
| |
| − | conf_gen_dn.o library_file.cpp score_descriptor.cpp utils.cpp
| |
| − | conf_gen_ga.cpp library_file.h score_descriptor.h utils.h
| |
| − | conf_gen_ga.h limit_max_change.cpp score_footprint.cpp version.h
| |
| − | conf_gen_ga.o limit_max_change.h score_footprint.h xlogp.cpp
| |
| − | conf_gen_hdb.cpp lol score_gist.cpp xlogp.h
| |
| − | conf_gen_hdb.h Makefile score_gist.h
| |
| − | (base) [ehspector@dn033 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn033 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn033 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Sun Feb 16 18:14:22 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | makIn file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dockmol.cpp: In function ‘bool Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)’:
| |
| − | dockmol.cpp:919:29: error: request for member ‘mol_status’ in ‘filter.Filter::gasteigerize’, which is of non-class type ‘bool’
| |
| − | 919 | if (filter.gasteigerize.mol_status = false){
| |
| − | | ^12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | make[1]: *** [../../install/rules.h:36: dockmol.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn033 install]$ cd ../../
| |
| − | (base) [ehspector@dn033 builds]$ cd alpha_branch/src/dock
| |
| − | (base) [ehspector@dn033 dock]$ vi filter.h
| |
| − | (base) [ehspector@dn033 dock]$ exit
| |
| − | exit
| |
| − | (base) [ehspector@milan2 dock]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Permission denied, please try again.
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ home
| |
| − | (base) [ehspector@milan2 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@milan2 espector]$ cd builds/alpha_branch/src/dock
| |
| − | (base) [ehspector@milan2 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@milan2 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@milan2 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@milan2 dock]$ rd
| |
| − | srun: job 932106 queued and waiting for resources
| |
| − | srun: job 932106 has been allocated resources
| |
| − | (base) [ehspector@dn035 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn035 install]$ ls
| |
| − | bluegenel gnu.acml homebrew intel.mkl sgi
| |
| − | bluegenep gnu.gdb homebrew.rdkit intel.parallel sgi.parallel
| |
| − | config.h gnu.parallel ibmaix Makefile test
| |
| − | configure gnu.parallel.rdkit intel oneapi
| |
| − | docker gnu.rdkit intel.intelmpi.parallel pgi
| |
| − | gnu gnu.valgrind intel.ip.mkl rules.h
| |
| − | (base) [ehspector@dn035 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn035 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Mon Feb 17 10:08:08 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from filter.h:10,
| |
| − | from filter.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_functio’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from filter.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | filter.cpp:214:7: error: expected unqualified-id before ‘else’
| |
| − | 214 | } else {
| |
| − | | ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | filter.cpp:221:5: error: ‘message’ does not name a type
| |
| − | 221 | message = get_descriptors(mol);
| |
| − | | ^12:36, 21 February 2025 (EST)~
| |
| − | filter.cpp:222:5: error: ‘cout’ does not name a type
| |
| − | 222 | cout << message << endl;
| |
| − | | ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | filter.cpp:223:1: error: expected declaration before ‘}’ token
| |
| − | 223 | }
| |
| − | | ^
| |
| − | make[1]: *** [../../install/rules.h:36: filter.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn035 install]$ module load git
| |
| − | (base) [ehspector@dn035 install]$ git diff
| |
| − | diff --git a/docs/new_in_6.13.txt b/docs/new_in_6.13.txt
| |
| − | index 7b10f318..fac269c6 100644
| |
| − | --- a/docs/new_in_6.13.txt
| |
| − | +++ b/docs/new_in_6.13.txt
| |
| − | @@ -29,6 +29,14 @@ Ligand Efficiency added for Descriptor Score
| |
| − | Users can now toggle ligand efficiency on/off when using grid_score in descriptor score.
| |
| − | Ligand efficiency can be used alongside with grid score and will be calculated as the grid score divided by the number of heavy atoms.
| |
| − |
| |
| − | +Gasterization of molecules in database filter
| |
| − | + Users can now apply gasteiger charges using the databasefilter question tree
| |
| − | + instead of having to gasterize molecules through the GA. This will be a useful
| |
| − | + tool in benchmarking dock as well as understanding the electrostatics of a
| |
| − | + protein environment.
| |
| − | + Disclaimer: gasterization can be used as long as the molecule is precharged
| |
| − | + and acts mainly as an interconversion function.
| |
| − | +
| |
| − | Miscellaneous
| |
| − |
| |
| − | Mutation Selection algorithmic changes for DOCK_GA
| |
| − | @@ -36,6 +44,8 @@ Mutation Selection algorithmic changes for DOCK_GA
| |
| − | the GA will not select a mutation type and then select a fragment
| |
| − | incompatible with the selected mutation type.
| |
| − |
| |
| − | +If users use sphere files, DOCK6 will print out the number of spheres used.
| |
| − | +
| |
| − | 12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − |
| |
| − | BUG FIXES
| |
| − | @@ -67,6 +77,8 @@ definitions added:
| |
| − | definition N.am
| |
| − | ______________________________________________________________________
| |
| − |
| |
| − | +Pertaining to the RDKit compilation with DOCK6, previous versions of DOCK6 included
| |
| − | +a broken Boost url for download. Hence, we have replaced it with a working url.
| |
| − |
| |
| − | 12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − |
| |
| − | @@ -88,6 +100,8 @@ For DOCK_GA:
| |
| − | ga_constraint_lower_mol_wt [0]
| |
| − | ga_constraint_lower_mol_wt [0]
| |
| − | ga_constraint_mol_wt_std_dev [35.0]
| |
| − |
| |
| − | +For Database Filter:
| |
| − | + dbfilter_gasteiger_charges [no] (yes no)
| |
| − |
| |
| − | 12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − |
| |
| − | @@ -111,6 +125,10 @@ KNOWN BUGS
| |
| − | 3. In the flex.defn file, there is a flag minimize which is disabled.
| |
| − | (The flag has no impact on the calculation.) All torsions are
| |
| − | Minimized.
| |
| − | +
| |
| − | + 4. Gasterization can be used as long as the molecule is precharged
| |
| − | + and acts mainly as an interconversion function.Additionally,ions
| |
| − | + will give calculating difficulty.
| |
| − |
| |
| − | 12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − |
| |
| − | diff --git a/src/dock/dockmol.cpp b/src/dock/dockmol.cpp
| |
| − | index 34811840..2f964a80 100644
| |
| − | --- a/src/dock/dockmol.cpp
| |
| − | +++ b/src/dock/dockmol.cpp
| |
| − | @@ -35,7 +35,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
| |
| − | #include <iomanip>
| |
| − | #include <string.h>
| |
| − | #include "dockmol.h"
| |
| − | -
| |
| − | +#include "filter.h"
| |
| − | #ifdef BUILD_DOCK_WITH_RDKIT
| |
| − | #include <fstream>
| |
| − | // RDKit stuff
| |
| − | @@ -539,14 +539,14 @@ Read_Mol2_retain(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvat
| |
| − | mol.subst_names[i] = subst_name;//mol.title
| |
| − | }
| |
| − | }
| |
| − | - // If all partial charges are zero, it is a bad molecule
| |
| − | + //If all partial charges are zero, it is a bad molecule
| |
| − | int num_zeros = 0;
| |
| − | for (int i = 0; i < mol.num_atoms; ++i){
| |
| − | if (mol.charges[i] == 0.0){
| |
| − | num_zeros += 1;
| |
| − | }
| |
| − | }
| |
| − | - // Is it a bad molecule?
| |
| − | + //Is it a bad molecule?
| |
| − | if (num_zeros == mol.num_atoms){
| |
| − | mol.bad_molecule = true;
| |
| − | }
| |
| − | - // Is it a bad molecule?
| |
| − | + //Is it a bad molecule?
| |
| − | if (num_zeros == mol.num_atoms){
| |
| − | mol.bad_molecule = true;
| |
| − | } else {
| |
| − | @@ -775,7 +775,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,
| |
| − | bool check_cols = false;
| |
| − | bool seven_columns = false; // default @<TRIPOS>ATOM line has 9 columns. By GDRM
| |
| − | //int bad_line{0}; // number of bad atom lines. By GDRM
| |
| − | -
| |
| − | + //declaring classes for gasteiger bypass EHS 2/16/25
| |
| − | + Filter filter;
| |
| − | + Filter mol_status;
| |
| − | // init state vars
| |
| − | atom_line = false;
| |
| − |
| |
| − | @@ -913,6 +915,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,
| |
| − | }
| |
| − | }
| |
| − | // If all partial charges are zero, it is a bad molecule
| |
| − | + // Skip over if gasterizing a molecule with no charges EHS 2/13/25
| |
| − | + if (filter.gasteigerize){
| |
| − | + goto skip;
| |
| − | int num_zeros = 0;
| |
| − | for (int i = 0; i < mol.num_atoms; ++i){
| |
| − | if (mol.charges[i] == 0.0){
| |
| − | @@ -925,6 +930,9 @@ Read_Mol2(DOCKMol & mol, istream & ifs, bool read_color, bool read_solvation,
| |
| − | } else {
| |
| − | mol.bad_molecule = false;
| |
| − | }
| |
| − | +}
| |
| − | + skip:
| |
| − | + cout << "This Molecule has no charges and will be gasterized" << endl;
| |
| − |
| |
| − | // skip down to the bond section
| |
| − | for (;;) {
| |
| − | diff --git a/src/dock/filter.cpp b/src/dock/filter.cpp
| |
| − | index b8469418..58f9c742 100644
| |
| − | --- a/src/dock/filter.cpp
| |
| − | +++ b/src/dock/filter.cpp
| |
| − | @@ -196,14 +196,14 @@ void Filter::calc_descriptors(DOCKMol & mol, AMBER_TYPER & c_typer)
| |
| − | }
| |
| − |
| |
| − | // placing a gasteiger flag this will be similar to ga code
| |
| − | - if ( gasteigerize ){
| |
| − | - //Establishing a temporary fingerprint and and compute atom environments (just like in GA) EHS 1/14/25
| |
| − | - activate_mol(mol);
| |
| − | + if ( gasteigerize && mol.bad_molecule == false ){
| |
| − | + //Establishing a temporary fingerprint and and compute atom environments (just like in GA) EHS 1/14/25
| |
| − | + activate_mol(mol);
| |
| − | (base) [ehspector@dn035 install]$
| |
| − | (base) [ehspector@dn035 install]$ exit
| |
| − | exit
| |
| − | (base) [ehspector@milan2 dock]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ home
| |
| − | (base) [ehspector@milan2 espector]$ cd 4s0v/
| |
| − | (base) [ehspector@milan2 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@milan2 4s0v]$ cd gas_teiger/
| |
| − | (base) [ehspector@milan2 gas_teiger]$ ls
| |
| − | 1AAQ_yesG.mol2 gas_3.out_scored.mol2 gas_5.out_scored.mol2 no_gas.in
| |
| − | gas_2.in gas_4.out gas.in no_gas.out
| |
| − | gas_2.out gas_4.out_scored.mol2 gas.out no_gas.out_scored.mol2
| |
| − | gas_2.out_scored.mol2 gas_5.in gas.out_scored.mol2 test
| |
| − | gas_3.out gas_5.out no_charge test.mol2
| |
| − | (base) [ehspector@milan2 gas_teiger]$ cd test/
| |
| − | (base) [ehspector@milan2 test]$ ls
| |
| − | 1AAQ_noG.mol2 gas_3.out gas_4.in gas_4.out_scored.mol2
| |
| − | gas_3.in gas_3.out_scored.mol2 gas_4.out test_nocharge.mol2
| |
| − | (base) [ehspector@milan2 test]$ vi gas_4.out
| |
| − | (base) [ehspector@milan2 test]$ vi gas_4.out_scored.mol2
| |
| − | (base) [ehspector@milan2 test]$ dock6 -i gas_4.in -o gas_4.out
| |
| − | (base) [ehspector@milan2 test]$ vi gas_4.out_scored.mol2
| |
| − | (base) [ehspector@milan2 test]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ home
| |
| − | (base) [ehspector@milan1 espector]$ cd 4s0v/
| |
| − | (base) [ehspector@milan1 4s0v]$ ls
| |
| − | cartesian_minimization fixed_anchor_docking footprint genericDenovo surface_spheres
| |
| − | Denovodata flex_docking fragLib gridbox virtual_screening
| |
| − | deNovorefinement flex_docking_mpi GA reScore
| |
| − | dock6_v_dock6mpi focusGrowth GA_data rigid_docking
| |
| − | energy_min focusReScore gas_teiger structure
| |
| − | (base) [ehspector@milan1 4s0v]$ cd ../builds/alpha_branch/src/
| |
| − | (base) [ehspector@milan1 src]$ cd dock
| |
| − | (base) [ehspector@milan1 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dock.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@milan1 dock]$ grep -wc Read_Mol2 *
| |
| − | amber_typer.cpp:0
| |
| − | amber_typer.h:0
| |
| − | amber_typer.o:0
| |
| − | base_grid.cpp:0
| |
| − | base_grid.h:0
| |
| − | base_grid.o:0
| |
| − | base_mpi.cpp:0
| |
| − | base_mpi.h:0
| |
| − | base_mpi.o:0
| |
| − | base_score.cpp:0
| |
| − | base_score.h:0
| |
| − | base_score.o:0
| |
| − | conf_gen_ag.cpp:0
| |
| − | conf_gen_ag.h:0
| |
| − | conf_gen_ag.o:0
| |
| − | conf_gen_cg.cpp:0
| |
| − | conf_gen_cg.h:0
| |
| − | conf_gen_cg.o:0
| |
| − | conf_gen_dn.cpp:2
| |
| − | conf_gen_dn_ga.cpp:1
| |
| − | conf_gen_dn_ga.h:0
| |
| − | conf_gen_dn_ga.o:0
| |
| − | conf_gen_dn.h:0
| |
| − | conf_gen_dn.o:0
| |
| − | conf_gen_ga.cpp:1
| |
| − | conf_gen_ga.h:0
| |
| − | conf_gen_ga.o:0
| |
| − | conf_gen_hdb.cpp:0
| |
| − | conf_gen_hdb.h:0
| |
| − | conf_gen_hdb.o:0
| |
| − | defreal.h:0
| |
| − | dock.cpp:0
| |
| − | dockmol.cpp:1
| |
| − | dockmol.h:1
| |
| − | dockmol.o:0
| |
| − | dock.o:0
| |
| − | filter.cpp:0
| |
| − | filter.h:0
| |
| − | fingerprint.cpp:1
| |
| − | fingerprint.h:0
| |
| − | fraggraph.cpp:0
| |
| − | fraggraph.h:0
| |
| − | fragment.cpp:0
| |
| − | fragment.h:0
| |
| − | gasteiger.cpp:0
| |
| − | gasteiger.h:0
| |
| − | grid.cpp:0
| |
| − | grid.h:0
| |
| − | grep: gzstream: Is a directory
| |
| − | gzstream:0
| |
| − | hungarian.cpp:0
| |
| − | hungarian.h:0
| |
| − | iso_align.cpp:0
| |
| − | iso_align.h:0
| |
| − | library_file.cpp:2
| |
| − | library_file.h:0
| |
| − | limit_max_change.cpp:0
| |
| − | limit_max_change.h:0
| |
| − | lol:0
| |
| − | Makefile:0
| |
| − | master_conf.cpp:0
| |
| − | master_conf.h:0
| |
| − | master_score.cpp:0
| |
| − | master_score.h:0
| |
| − | mem_info.cpp:0
| |
| − | mem_info.h:0
| |
| − | grep: nab: Is a directory
| |
| − | nab:0
| |
| − | nabcode.h:0
| |
| − | nab.h:0
| |
| − | orient.cpp:0
| |
| − | orient.h:0
| |
| − | rddrive.cpp:0
| |
| − | rddrive.h:0
| |
| − | rdtyper.cpp:0
| |
| − | rdtyper.h:0
| |
| − | README:0
| |
| − | sasa.cpp:0
| |
| − | sasa.h:0
| |
| − | score_amber.cpp:0
| |
| − | score_amber.h:0
| |
| − | score_chemgrid.cpp:0
| |
| − | score_chemgrid.h:0
| |
| − | score.cpp:1
| |
| − | score_descriptor.cpp:2
| |
| − | score_descriptor.h:0
| |
| − | score_footprint.cpp:2
| |
| − | score_footprint.h:0
| |
| − | score_gist.cpp:0
| |
| − | score_gist.h:0
| |
| − | score.h:0
| |
| − | score_hbond.cpp:1
| |
| − | score_hbond.h:0
| |
| − | score_internal.cpp:0
| |
| − | score_internal.h:0
| |
| − | score_multigrid.cpp:1
| |
| − | score_multigrid.h:0
| |
| − | score_ph4.cpp:2
| |
| − | score_ph4.h:0
| |
| − | score_sasa.cpp:1
| |
| − | score_sasa.h:0
| |
| − | score_solvent.cpp:1
| |
| − | score_solvent.h:0
| |
| − | score_volume.cpp:1
| |
| − | score_volume.h:0
| |
| − | simplex.cpp:0
| |
| − | simplex.h:0
| |
| − | sphere.cpp:0
| |
| − | sphere.h:0
| |
| − | grep: tnt: Is a directory
| |
| − | tnt:0
| |
| − | trace.cpp:0
| |
| − | trace.h:0
| |
| − | trace.inl:0
| |
| − | utils.cpp:0
| |
| − | utils.h:0
| |
| − | version.h:0
| |
| − | xlogp.cpp:0
| |
| − | xlogp.h:0
| |
| − | (base) [ehspector@milan1 dock]$ vi library_file.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dock.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dock.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dock.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi library_file.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dock.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dock.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi library_file.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi filter.h
| |
| − | (base) [ehspector@milan1 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi filter.h
| |
| − | (base) [ehspector@milan1 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@milan1 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@milan1 dock]$ rd
| |
| − | srun: job 932383 queued and waiting for resources
| |
| − | srun: job 932383 has been allocated resources
| |
| − | (base) [ehspector@dn051 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn051 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn051 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Mon Feb 17 12:54:43 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from filter.h:10,
| |
| − | from filter.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from filter.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | filter.cpp:214:7: error: expected unqualified-id before ‘else’
| |
| − | 214 | } else {
| |
| − | | ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | filter.cpp:221:5: error: ‘message’ does not name a type
| |
| − | 221 | message = get_descriptors(mol);
| |
| − | | ^12:36, 21 February 2025 (EST)~
| |
| − | filter.cpp:222:5: error: ‘cout’ does not name a type
| |
| − | 222 | cout << message << endl;
| |
| − | | ^[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | filter.cpp:223:1: error: expected declaration before ‘}’ token
| |
| − | 223 | }
| |
| − | | ^
| |
| − | make[1]: *** [../../install/rules.h:36: filter.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn051 install]$ cd ../../
| |
| − | (base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock
| |
| − | (base) [ehspector@dn051 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@dn051 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn051 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn051 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Mon Feb 17 13:00:19 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from filter.h:10,
| |
| − | from filter.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from filter.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | filter.cpp: In member function ‘void Filter::calc_descriptors(DOCKMol&, AMBER_TYPER&)’:
| |
| − | filter.cpp:279:26: error: qualified-id in declaration before ‘(’ token
| |
| − | 279 | bool Filter::fails_filter(DOCKMol & mol)
| |
| − | | ^
| |
| − | filter.cpp:529:31: error: qualified-id in declaration before ‘(’ token
| |
| − | 529 | string Filter::get_descriptors(DOCKMol & mol)
| |
| − | | ^
| |
| − | filter.cpp:591:21: error: qualified-id in declaration before ‘(’ token
| |
| − | 591 | Filter::activate_mol( DOCKMol & mol )
| |
| − | | ^
| |
| − | filter.cpp:605:2: error: expected ‘}’ at end of input
| |
| − | 605 | } // end Filter::activate_mol()
| |
| − | | ^
| |
| − | filter.cpp:147:1: note: to match this ‘{’
| |
| − | 147 | {
| |
| − | | ^
| |
| − | make[1]: *** [../../install/rules.h:36: filter.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn051 install]$ cd ../../alpha_branch/src/dock
| |
| − | (base) [ehspector@dn051 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@dn051 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn051 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn051 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Mon Feb 17 13:05:08 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from filter.h:10,
| |
| − | from filter.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from filter.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fingerprint.h:13,
| |
| − | from fingerprint.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from fingerprint.h:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fraggraph.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fraggraph.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fragment.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fragment.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from gasteiger.h:8,
| |
| − | from gasteiger.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from gasteiger.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from hungarian.h:7,
| |
| − | from hungarian.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from hungarian.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from library_file.h:9,
| |
| − | from library_file.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from library_file.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o limit_max_change.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from limit_max_change.h:12,
| |
| − | from limit_max_change.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from limit_max_change.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o master_conf.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from master_conf.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from master_conf.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o master_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from master_score.h:5,
| |
| − | from master_score.cpp:2:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from master_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o orient.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from orient.h:7,
| |
| − | from orient.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from orient.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o sasa.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from sasa.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from sasa.h:14:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o score_amber.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_amber.cpp:66:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
| |
| − | from score_amber.cpp:55:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o score_chemgrid.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_chemgrid.cpp:39:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
| |
| − | from score_chemgrid.cpp:38:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o score_descriptor.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_descriptor.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_descriptor.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o score_footprint.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_footprint.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_footprint.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o score_ph4.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_ph4.h:7,
| |
| − | from score_ph4.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_ph4.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o score_volume.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_volume.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_volume.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o score_gist.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_gist.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_gist.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o score_hbond.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_hbond.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_hbond.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o score_internal.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_internal.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_internal.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o score_multigrid.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_multigrid.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_multigrid.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o score_sasa.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from score_sasa.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_sasa.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o score_solvent.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from score_solvent.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_solvent.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o simplex.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from master_score.h:5,
| |
| − | from simplex.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from simplex.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o sphere.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o trace.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o utils.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from utils.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from utils.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o iso_align.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fragment.h:12,
| |
| − | from iso_align.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from fragment.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o mem_info.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o rdtyper.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
| |
| − | from rdtyper.cpp:18:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from rdtyper.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o rddrive.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from rddrive.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from dockmol.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | cd nab && make all
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | gcc -c -O3 -D_ANSI_SOURCE molio.c
| |
| − | gcc -c -O2 -o prm.o prm.c
| |
| − | make is_LEX_available
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c
| |
| − | gcc -c -O2 -o traceback.o traceback.c
| |
| − | gcc -c -O2 -o select_atoms.o select_atoms.c
| |
| − | gcc -c -O2 -o memutil.o memutil.c
| |
| − | gcc -c -O2 -o reslib.o reslib.c
| |
| − | gcc -c -O2 -o jacobi.o jacobi.c
| |
| − | gcc -c -O2 -o molutil.o molutil.c
| |
| − | gcc -c -O2 -o chirvol.o chirvol.c
| |
| − | gcc -c -O2 -o regexp.o regexp.c
| |
| − | gcc -c -O2 -o binpos.o binpos.c
| |
| − | gcc -c -O2 -o time.o time.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE rand2.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE conjgrad.c
| |
| − | gcc -c -O2 -o database.o database.c
| |
| − | gcc -c -O2 -o tleap.o tleap.c
| |
| − | ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
| |
| − | ar: creating nab.a
| |
| − | a - molio.o
| |
| − | a - prm.o
| |
| − | a - sff.o
| |
| − | a - traceback.o
| |
| − | a - select_atoms.o
| |
| − | a - memutil.o
| |
| − | a - reslib.o
| |
| − | a - jacobi.o
| |
| − | a - molutil.o
| |
| − | a - chirvol.o
| |
| − | a - regexp.o
| |
| − | a - binpos.o
| |
| − | a - time.o
| |
| − | a - rand2.o
| |
| − | a - conjgrad.o
| |
| − | a - database.o
| |
| − | a - tleap.o
| |
| − | ranlib nab.a
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
| |
| − | ar cr libgzstream.a gzstream.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
| |
| − | -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
| |
| − | mv dock6.rdkit ../../bin
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − |
| |
| − | Installation of
| |
| − | DOCK v6.12
| |
| − | program dock is complete at Mon Feb 17 13:08:09 EST 2025.
| |
| − |
| |
| − | (base) [ehspector@dn051 install]$ cd ../al
| |
| − | bash: cd: ../al: No such file or directory
| |
| − | (base) [ehspector@dn051 install]$ cd ../../alpha_branch/
| |
| − | (base) [ehspector@dn051 alpha_branch]$ cd src/dock
| |
| − | (base) [ehspector@dn051 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi filter.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi dock.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi library_file.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn051 dock]$ cd ../../
| |
| − | (base) [ehspector@dn051 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@dn051 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn051 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Mon Feb 17 13:31:34 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dock.cpp: In function ‘int main(int, char**)’:
| |
| − | dock.cpp:785:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool&, bool&, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
| |
| − | 785 | while (c_library.get_mol(mol,c_filter.use_database_filter,c_filter.gasterize, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
| |
| − | | 12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | In file included from dock.cpp:62:
| |
| − | library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
| |
| − | 141 | bool get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
| |
| − | | ^12:36, 21 February 2025 (EST)~
| |
| − | library_file.h:141:21: note: candidate expects 7 arguments, 8 provided
| |
| − | make[1]: *** [../../install/rules.h:36: dock.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn051 install]$ cd ../
| |
| − | (base) [ehspector@dn051 alpha_branch]$ cd ../
| |
| − | (base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock
| |
| − | (base) [ehspector@dn051 dock]$ vi dock.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi library_file.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn051 dock]$ ls
| |
| − | amber_typer.cpp conf_gen_dn.o gzstream rddrive.h score_multigrid.h
| |
| − | amber_typer.h conf_gen_ga.cpp hungarian.cpp rdtyper.cpp score_ph4.cpp
| |
| − | amber_typer.o conf_gen_ga.h hungarian.h rdtyper.h score_ph4.h
| |
| − | base_grid.cpp conf_gen_ga.o iso_align.cpp README score_sasa.cpp
| |
| − | base_grid.h conf_gen_hdb.cpp iso_align.h sasa.cpp score_sasa.h
| |
| − | base_grid.o conf_gen_hdb.h library_file.cpp sasa.h score_solvent.cpp
| |
| − | base_mpi.cpp conf_gen_hdb.o library_file.h score_amber.cpp score_solvent.h
| |
| − | base_mpi.h defreal.h limit_max_change.cpp score_amber.h score_volume.cpp
| |
| − | base_mpi.o dock.cpp limit_max_change.h score_chemgrid.cpp score_volume.h
| |
| − | base_score.cpp dockmol.cpp lol score_chemgrid.h simplex.cpp
| |
| − | base_score.h dockmol.h Makefile score.cpp simplex.h
| |
| − | base_score.o filter.cpp master_conf.cpp score_descriptor.cpp sphere.cpp
| |
| − | conf_gen_ag.cpp filter.h master_conf.h score_descriptor.h sphere.h
| |
| − | conf_gen_ag.h fingerprint.cpp master_score.cpp score_footprint.cpp tnt
| |
| − | conf_gen_ag.o fingerprint.h master_score.h score_footprint.h trace.cpp
| |
| − | conf_gen_cg.cpp fraggraph.cpp mem_info.cpp score_gist.cpp trace.h
| |
| − | conf_gen_cg.h fraggraph.h mem_info.h score_gist.h trace.inl
| |
| − | conf_gen_cg.o fragment.cpp nab score.h utils.cpp
| |
| − | conf_gen_dn.cpp fragment.h nabcode.h score_hbond.cpp utils.h
| |
| − | conf_gen_dn_ga.cpp gasteiger.cpp nab.h score_hbond.h version.h
| |
| − | conf_gen_dn_ga.h gasteiger.h orient.cpp score_internal.cpp xlogp.cpp
| |
| − | conf_gen_dn_ga.o grid.cpp orient.h score_internal.h xlogp.h
| |
| − | conf_gen_dn.h grid.h rddrive.cpp score_multigrid.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi dockmol.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi dock.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi library_file.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi dock.cpp
| |
| − | (base) [ehspector@dn051 dock]$ cd ../../
| |
| − | (base) [ehspector@dn051 alpha_branch]$ cd install/
| |
| − | (base) [ehspector@dn051 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn051 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Mon Feb 17 13:40:15 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | dock.cpp: In function ‘int main(int, char**)’:
| |
| − | dock.cpp:340:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool, bool, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
| |
| − | 340 | while (c_library.get_mol(mol, false, false, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
| |
| − | | 12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)
| |
| − | In file included from dock.cpp:62:
| |
| − | library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
| |
| − | 141 | bool get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
| |
| − | | ^12:36, 21 February 2025 (EST)~
| |
| − | library_file.h:141:21: note: candidate expects 7 arguments, 8 provided
| |
| − | dock.cpp:785:29: error: no matching function for call to ‘Library_File::get_mol(DOCKMol&, bool&, bool&, bool&, bool&, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
| |
| − | 785 | while (c_library.get_mol(mol,c_filter.use_database_filter,c_filter.gasterize, USE_MPI, c_master_score.amber, c_typer, c_master_score, c_simplex)) {
| |
| − | | 12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~~^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]]) 12:36, 21 February 2025 (EST)
| |
| − | library_file.h:141:21: note: candidate: ‘bool Library_File::get_mol(DOCKMol&, bool, bool, bool, AMBER_TYPER&, Master_Score&, Simplex_Minimizer&)’
| |
| − | 141 | bool get_mol(DOCKMol &,bool, bool, bool, AMBER_TYPER &, Master_Score &, Simplex_Minimizer &);
| |
| − | | ^12:36, 21 February 2025 (EST)~
| |
| − | library_file.h:141:21: note: candidate expects 7 arguments, 8 provided
| |
| − | make[1]: *** [../../install/rules.h:36: dock.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn051 install]$ cd ..
| |
| − | (base) [ehspector@dn051 alpha_branch]$ cd ..
| |
| − | (base) [ehspector@dn051 builds]$ cd alpha_branch/src/dock
| |
| − | (base) [ehspector@dn051 dock]$ vi library_file.h
| |
| − | (base) [ehspector@dn051 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn051 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | make -C resp clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
| |
| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make -C chemgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
| |
| − | make -C solvgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn051 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Mon Feb 17 13:45:32 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from filter.h:10,
| |
| − | from filter.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from filter.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fingerprint.h:13,
| |
| − | from fingerprint.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from fingerprint.h:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fraggraph.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fraggraph.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fragment.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fragment.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from gasteiger.h:8,
| |
| − | from gasteiger.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from gasteiger.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from hungarian.h:7,
| |
| − | from hungarian.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from hungarian.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from library_file.h:9,
| |
| − | from library_file.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from library_file.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | library_file.cpp: In member function ‘void Library_File::open_files()’:
| |
| − | library_file.cpp:1384:21: error: no matching function for call to ‘Library_File::read_mol(DOCKMol&, bool’
| |
| − | 1384 | if (read_mol(tmp_mol, false))
| |
| − | | 12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)
| |
| − | library_file.h:139:21: note: candidate: ‘bool Library_File::read_mol(DOCKMol&, bool, bool)’
| |
| − | 139 | bool read_mol(DOCKMol &, bool, bool); //Accomodating gasteiger input EHS 2/17/25
| |
| − | | ^12:36, 21 February 2025 (EST)~~
| |
| − | library_file.h:139:21: note: candidate expects 3 arguments, 2 provided
| |
| − | library_file.cpp: At global scope:
| |
| − | library_file.cpp:1435:1: error: no declaration matches ‘bool Library_File::read_mol(DOCKMol&, bool)’
| |
| − | 1435 | Library_File::read_mol(DOCKMol & mol, bool read_amber)
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~
| |
| − | library_file.h:139:21: note: candidate is: ‘bool Library_File::read_mol(DOCKMol&, bool, bool)’
| |
| − | 139 | bool read_mol(DOCKMol &, bool, bool); //Accomodating gasteiger input EHS 2/17/25
| |
| − | | ^12:36, 21 February 2025 (EST)~~
| |
| − | library_file.h:19:17: note: ‘class Library_File’ defined here
| |
| − | 19 | class Library_File:public Base_MPI {
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)~
| |
| − | make[1]: *** [../../install/rules.h:36: library_file.o] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn051 install]$ cd ..
| |
| − | (base) [ehspector@dn051 alpha_branch]$ cd src/dock
| |
| − | (base) [ehspector@dn051 dock]$ vi dock.cpp
| |
| − | (base) [ehspector@dn051 dock]$ vi library_file.cpp
| |
| − | (base) [ehspector@dn051 dock]$ cd ../../install/
| |
| − | (base) [ehspector@dn051 install]$ make clean
| |
| − | make -C ../src clean
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | make -C dock clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | /bin/rm -f amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o
| |
| − | cd nab && make clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | /bin/rm -f *.o nab.a lex.mm_options.c
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make cleanall
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | /bin/rm -f *.o libgzstream.a test_gzip test_gunzip
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make -C accessories clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | /bin/rm -f showbox.o showsphere.o sphgen.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/accessories'
| |
| − | make -C gbsa_grids clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C schemgrid_GB clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_GB'
| |
| − | make -C schemgrid_SA clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | /bin/rm -f nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids/schemgrid_SA'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/gbsa_grids'
| |
| − | make -C grid clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | /bin/rm -f grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/grid'
| |
| − | make -C tleap clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | /bin/rm -f teLeap utilMakeHelp *.o parser.c helptext.c
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/tleap'
| |
| − | make -C antechamber clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | /bin/rm -f *.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/antechamber'
| |
| − | make -C mopac6/src clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
| |
| − | /bin/rm -f aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o geout.o geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o mullik.o mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o refer.o repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o wrttxt.o xyzint.o
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/mopac6/src'
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| − | make -C resp clean
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| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
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| − | /bin/rm -f amopen.o lapack.o mexit.o resp.o
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| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/resp'
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| − | make -C docktools clean
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
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| − | make -C chemgrids clean
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| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
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| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
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| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/chemgrids'
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| − | make -C solvgrids clean
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| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
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| − | /bin/rm -f chemgrid.o dist.o ddist.o dconst.o grdout.o parmrec.o
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| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids'
| |
| − | make -C solvgrids_sev clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
| |
| − | /bin/rm -f sas.o cube.o memalloc.o solvmap.o
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/solvgrids_sev'
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| − | make -C convgrids clean
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
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| − | make -f gridconv.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
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| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
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| − | make -f gridrdsl.mk clean
| |
| − | make[4]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | /bin/rm -f grid.o io_grid.o io_gridf.o label.o label_node.o label_chem.o label_vdw.o parm.o parm_grid.o utility.o
| |
| − | make[4]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools/convgrids'
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/docktools'
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src'
| |
| − | (base) [ehspector@dn051 install]$ make dock
| |
| − | Starting installation of
| |
| − | DOCK v6.12
| |
| − | program dock at Mon Feb 17 13:53:32 EST 2025.
| |
| − |
| |
| − | make -C ../src/dock install
| |
| − | make[1]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o amber_typer.o amber_typer.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from amber_typer.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from amber_typer.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_grid.o base_grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_mpi.o base_mpi.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_mpi.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/sstream:40,
| |
| − | from base_mpi.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o base_score.o base_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from base_score.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from base_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ag.o conf_gen_ag.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ag.h:5,
| |
| − | from conf_gen_ag.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ag.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_cg.o conf_gen_cg.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_cg.h:5,
| |
| − | from conf_gen_cg.cpp:17:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_cg.cpp:8:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn.o conf_gen_dn.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn.h:12,
| |
| − | from conf_gen_dn.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_dn_ga.o conf_gen_dn_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_dn_ga.h:12,
| |
| − | from conf_gen_dn_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_dn_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_ga.o conf_gen_ga.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_ga.h:13,
| |
| − | from conf_gen_ga.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from conf_gen_ga.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o conf_gen_hdb.o conf_gen_hdb.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from conf_gen_hdb.h:4,
| |
| − | from conf_gen_hdb.cpp:14:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from conf_gen_hdb.cpp:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dock.o dock.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from dock.cpp:61:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dock.cpp:53:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o dockmol.o dockmol.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from dockmol.cpp:37:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from dockmol.cpp:33:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o filter.o filter.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from filter.h:10,
| |
| − | from filter.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from filter.h:4:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fingerprint.o fingerprint.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fingerprint.h:13,
| |
| − | from fingerprint.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from fingerprint.h:6:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fraggraph.o fraggraph.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fraggraph.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fraggraph.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o fragment.o fragment.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fragment.cpp:3:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from fragment.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o gasteiger.o gasteiger.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from gasteiger.h:8,
| |
| − | from gasteiger.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from gasteiger.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o grid.o grid.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o hungarian.o hungarian.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from hungarian.h:7,
| |
| − | from hungarian.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from hungarian.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o library_file.o library_file.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from library_file.h:9,
| |
| − | from library_file.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from library_file.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o limit_max_change.o limit_max_change.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from limit_max_change.h:12,
| |
| − | from limit_max_change.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from limit_max_change.h:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_conf.o master_conf.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from master_conf.h:6,
| |
| − | from master_conf.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from master_conf.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o master_score.o master_score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from master_score.h:5,
| |
| − | from master_score.cpp:2:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from master_score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o orient.o orient.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from orient.h:7,
| |
| − | from orient.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from orient.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sasa.o sasa.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from sasa.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from sasa.h:14:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score.o score.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_amber.o score_amber.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_amber.cpp:66:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
| |
| − | from score_amber.cpp:55:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_chemgrid.o score_chemgrid.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_chemgrid.cpp:39:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iomanip:42,
| |
| − | from score_chemgrid.cpp:38:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_descriptor.o score_descriptor.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_descriptor.cpp:10:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_descriptor.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_footprint.o score_footprint.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_footprint.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_footprint.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_ph4.o score_ph4.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_ph4.h:7,
| |
| − | from score_ph4.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_ph4.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_volume.o score_volume.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_volume.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_volume.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_gist.o score_gist.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_gist.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_gist.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_hbond.o score_hbond.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_hbond.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_hbond.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_internal.o score_internal.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_internal.cpp:8:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_internal.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_multigrid.o score_multigrid.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score_multigrid.cpp:9:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_multigrid.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_sasa.o score_sasa.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from score_sasa.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_sasa.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o score_solvent.o score_solvent.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from score_solvent.h:9,
| |
| − | from sasa.h:15,
| |
| − | from score_solvent.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from score_solvent.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o simplex.o simplex.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from score.h:7,
| |
| − | from master_score.h:5,
| |
| − | from simplex.cpp:4:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from simplex.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o sphere.o sphere.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o trace.o trace.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o utils.o utils.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from utils.cpp:7:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from utils.cpp:1:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o iso_align.o iso_align.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from fragment.h:12,
| |
| − | from iso_align.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/istream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/fstream:40,
| |
| − | from fragment.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o mem_info.o mem_info.cpp
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rdtyper.o rdtyper.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/GraphMol.h:19,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/RDKitBase.h:26,
| |
| − | from rdtyper.cpp:18:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/locale_classes.h:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:41,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
| |
| − | from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/iostream:41,
| |
| − | from rdtyper.cpp:2:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | g++ -c -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -o rddrive.o rddrive.cpp
| |
| − | In file included from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/functional/hash.hpp:6,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered/unordered_set.hpp:18,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/unordered_set.hpp:17,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/graph/adjacency_list.hpp:21,
| |
| − | from /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code/GraphMol/ROMol.h:27,
| |
| − | from dockmol.h:16,
| |
| − | from rddrive.cpp:1:
| |
| − | /gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
| |
| − | 130 | struct hash_base : std::unary_function<T, std::size_t> {};
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
| |
| − | from dockmol.h:5:
| |
| − | /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
| |
| − | 117 | struct unary_function
| |
| − | | ^12:36, 21 February 2025 (EST)12:36, 21 February 2025 (EST)[[User:Stonybrook|Stonybrook]] ([[User talk:Stonybrook|talk]])
| |
| − | cd nab && make all
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | gcc -c -O3 -D_ANSI_SOURCE molio.c
| |
| − | gcc -c -O2 -o prm.o prm.c
| |
| − | make is_LEX_available
| |
| − | make[3]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | make[3]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | flex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex -D_DARWIN_C_SOURCE -D_XOPEN_SOURCE=600 sff.c
| |
| − | gcc -c -O2 -o traceback.o traceback.c
| |
| − | gcc -c -O2 -o select_atoms.o select_atoms.c
| |
| − | gcc -c -O2 -o memutil.o memutil.c
| |
| − | gcc -c -O2 -o reslib.o reslib.c
| |
| − | gcc -c -O2 -o jacobi.o jacobi.c
| |
| − | gcc -c -O2 -o molutil.o molutil.c
| |
| − | gcc -c -O2 -o chirvol.o chirvol.c
| |
| − | gcc -c -O2 -o regexp.o regexp.c
| |
| − | gcc -c -O2 -o binpos.o binpos.c
| |
| − | gcc -c -O2 -o time.o time.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE rand2.c
| |
| − | gcc -c -O3 -D_ANSI_SOURCE conjgrad.c
| |
| − | gcc -c -O2 -o database.o database.c
| |
| − | gcc -c -O2 -o tleap.o tleap.c
| |
| − | ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o conjgrad.o database.o tleap.o
| |
| − | ar: creating nab.a
| |
| − | a - molio.o
| |
| − | a - prm.o
| |
| − | a - sff.o
| |
| − | a - traceback.o
| |
| − | a - select_atoms.o
| |
| − | a - memutil.o
| |
| − | a - reslib.o
| |
| − | a - jacobi.o
| |
| − | a - molutil.o
| |
| − | a - chirvol.o
| |
| − | a - regexp.o
| |
| − | a - binpos.o
| |
| − | a - time.o
| |
| − | a - rand2.o
| |
| − | a - conjgrad.o
| |
| − | a - database.o
| |
| − | a - tleap.o
| |
| − | ranlib nab.a
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/nab'
| |
| − | cd gzstream && make
| |
| − | make[2]: Entering directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -I. -O2 -std=c++11 -DBUILD_DOCK_WITH_RDKIT -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/Code -I/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/include -c -o gzstream.o gzstream.C
| |
| − | ar cr libgzstream.a gzstream.o
| |
| − | make[2]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock/gzstream'
| |
| − | g++ -O2 -o dock6.rdkit amber_typer.o base_grid.o base_mpi.o base_score.o conf_gen_ag.o conf_gen_cg.o conf_gen_dn.o conf_gen_dn_ga.o conf_gen_ga.o conf_gen_hdb.o dock.o dockmol.o filter.o fingerprint.o fraggraph.o fragment.o gasteiger.o grid.o hungarian.o library_file.o limit_max_change.o master_conf.o master_score.o orient.o sasa.o score.o score_amber.o score_chemgrid.o score_descriptor.o score_footprint.o score_ph4.o score_volume.o score_gist.o score_hbond.o score_internal.o score_multigrid.o score_sasa.o score_solvent.o simplex.o sphere.o trace.o utils.o iso_align.o mem_info.o rdtyper.o rddrive.o nab/*.o gzstream/gzstream.o -lz \
| |
| − | -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -L/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/boost/lib -Wl,-rpath=/gpfs/projects/rizzo/espector/builds/alpha_branch/src/rdkit/rdkit-Release_2019_09_1/lib -lm -lpthread -lstdc++ -lRDKitGraphMol -lRDKitRDGeneral -lRDKitDescriptors -lRDKitSmilesParse -lRDKitSubstructMatch -lRDKitChemTransforms -lRDKitFilterCatalog -lRDKitFingerprints -lRDKitFileParsers -lRDKitCatalogs
| |
| − | conf_gen_dn.o: In function `DN_Build::read_library(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
| |
| − | conf_gen_dn.cpp:(.text+0x1ec40): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
| |
| − | conf_gen_dn.o: In function `DN_Build::read_library_anchor(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
| |
| − | conf_gen_dn.cpp:(.text+0x1f508): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
| |
| − | conf_gen_dn_ga.o: In function `DN_GA_Build::read_library(std::vector<Fragment, std::allocator<Fragment> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
| |
| − | conf_gen_dn_ga.cpp:(.text+0xdf40): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
| |
| − | conf_gen_ga.o: In function `GA_Recomb::read_library(std::vector<DOCKMol, std::allocator<DOCKMol> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
| |
| − | conf_gen_ga.cpp:(.text+0x1d5c5): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
| |
| − | fingerprint.o: In function `Fingerprint::input_parameters(Parameter_Reader&)':
| |
| − | fingerprint.cpp:(.text+0x2f14): undefined reference to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)'
| |
| − | library_file.o:library_file.cpp:(.text+0x6c75): more undefined references to `Read_Mol2(DOCKMol&, std::istream&, bool, bool, bool)' follow
| |
| − | collect2: error: ld returned 1 exit status
| |
| − | make[1]: *** [Makefile:39: dock6.rdkit] Error 1
| |
| − | make[1]: Leaving directory '/gpfs/projects/rizzo/espector/builds/alpha_branch/src/dock'
| |
| − | make: *** [Makefile:28: dock] Error 2
| |
| − | (base) [ehspector@dn051 install]$ exiy
| |
| − | bash: exiy: command not found
| |
| − | (base) [ehspector@dn051 install]$ exit
| |
| − | exit
| |
| − | srun: error: dn051: task 0: Exited with exit code 127
| |
| − | (base) [ehspector@milan1 dock]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi commands.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ mkdir test
| |
| − | (base) [ehspector@milan1 AMS_536]$ mkdir test
| |
| − | mkdir: cannot create directory ‘test’: File exists
| |
| − | (base) [ehspector@milan1 AMS_536]$ mkdir move
| |
| − | (base) [ehspector@milan1 AMS_536]$ mv test/ move/
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt move Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ rm -r move
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi commands.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi Notes.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi commands.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd class_project/
| |
| − | (base) [ehspector@milan1 class_project]$ ls
| |
| − | (base) [ehspector@milan1 class_project]$ cd T
| |
| − | -bash: cd: T: No such file or directory
| |
| − | (base) [ehspector@milan1 class_project]$ ls
| |
| − | (base) [ehspector@milan1 class_project]$ cd ..
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar test4.tar
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min Robs_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_new_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ ls
| |
| − | 000_test 002_spheres 004_dock 006_ga_lib
| |
| − | 001_structure 003_grid 005_analysis 007_ga_run1
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ mkdir ga_calc
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar Robs_new_2w26
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min ga_calc test4.tar
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ vi N
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi Notes.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi Notes.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ cd Robs_new_2w26/
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ ls
| |
| − | 000_test 002_spheres 004_dock 006_ga_lib
| |
| − | 001_structure 003_grid 005_analysis 007_ga_run1
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd 006_ga_lib/
| |
| − | (base) [ehspector@milan1 006_ga_lib]$ ls
| |
| − | 01lib.sh 2W26.fraglib.out 2W26_fragout_scored.mol2
| |
| − | 02combine.sh 2W26_fraglib_rigid.mol2 full_fraglib.dat
| |
| − | 2W26.fraglib.in 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat
| |
| − | 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 unique_full_sorted_fraglib.dat
| |
| − | 2W26.fraglib.log 2W26_fraglib_torenv.dat
| |
| − | (base) [ehspector@milan1 006_ga_lib]$ vi 2W26.fraglib.in
| |
| − | (base) [ehspector@milan1 006_ga_lib]$ cd ..
| |
| − | (base) [ehspector@milan1 Robs_new_2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cp Robs_new_2w26/006_ga_lib/2W26.fraglib.in ga_calc/2w26_fraglib.in
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar Robs_new_2w26
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min ga_calc test4.tar
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cd 007_virtual_screen/
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ ls
| |
| − | virtual.in virtual.out virtual_scored.mol2 virtual.sh vs_output.txt
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ vi virtual.sh
| |
| − | (base) [ehspector@milan1 007_virtual_screen]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ cp 004_energymin/min.sh ga_calc/lib.sh
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar Robs_new_2w26
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min ga_calc test4.tar
| |
| − | 003_gridbox 006_footprint 009_rescore Robs_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cd ga_calc/
| |
| − | (base) [ehspector@milan1 ga_calc]$ ls
| |
| − | 2w26_fraglib.in lib.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi lib.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi lib.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in
| |
| − | (base) [ehspector@milan1 ga_calc]$ cd ../001_structure/
| |
| − | (base) [ehspector@milan1 001_structure]$ ls
| |
| − | 2w26_ligand_H_cH.mol2 2w26_protein_H_cH.mol2
| |
| − | 2w26_ligand_noH_nocH.mol2 2w26_protein_noH_nocH.mol2
| |
| − | (base) [ehspector@milan1 001_structure]$ cd ../ga_calc/
| |
| − | (base) [ehspector@milan1 ga_calc]$ ls
| |
| − | 2w26_fraglib.in lib.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.in
| |
| − | (base) [ehspector@milan1 ga_calc]$ bash lib.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ ls
| |
| − | 2w26_fraglib.in 2W26_fraglib_rigid.mol2 2W26_fraglib_sidechain.mol2
| |
| − | 2W26_fraglib_linker.mol2 2W26_fraglib_scaffold.mol2 2W26_fraglib_torenv.dat
| |
| − | 2w26_fraglib.out 2w26_fraglib_scored.mol2 lib.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi 2w26_fraglib.out
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi 2W26_fraglib_scaffold.mol2
| |
| − | (base) [ehspector@milan1 ga_calc]$ grep -c "lnk" 2W26_fraglib_linker.mol2
| |
| − | 51
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi 2W26_fraglib_linker.mol2
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi py.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi lib.sh.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi lib.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi py.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ ls
| |
| − | 2w26_fraglib.in 2W26_fraglib_rigid.mol2 2W26_fraglib_sidechain.mol2 py.sh
| |
| − | 2W26_fraglib_linker.mol2 2W26_fraglib_scaffold.mol2 2W26_fraglib_torenv.dat
| |
| − | 2w26_fraglib.out 2w26_fraglib_scored.mol2 lib.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi py.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ module load python
| |
| − | (base) [ehspector@milan1 ga_calc]$ bash py.sh
| |
| − | (base) [ehspector@milan1 ga_calc]$ ls
| |
| − | 2w26_fraglib.in 2w26_fraglib_scored.mol2 lib.sh
| |
| − | 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 py.sh
| |
| − | 2w26_fraglib.out 2W26_fraglib_torenv.dat unique_full_sorted_fraglib.dat
| |
| − | 2W26_fraglib_rigid.mol2 full_fraglib.dat
| |
| − | 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat
| |
| − | (base) [ehspector@milan1 ga_calc]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ mkdir ga_run
| |
| − | (base) [ehspector@milan1 2w26]$ cd ga_run/
| |
| − | (base) [ehspector@milan1 ga_run]$ ls
| |
| − | (base) [ehspector@milan1 ga_run]$ touch 2w26_ga.in
| |
| − | (base) [ehspector@milan1 ga_run]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):genetic
| |
| − |
| |
| − | Genetic Algorithm Recombination Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ga_molecule_file [ga_molecule_file.mol2] ():../001_structure/2w26_ligand_H_cH.mol2
| |
| − | ga_utilities [no] (yes no):
| |
| − | ga_fraglib_scaffold_file [fraglib_scaffold.mol2] ():
| |
| − | ga_fraglib_linker_file [fraglib_linker.mol2] ():
| |
| − | ga_fraglib_sidechain_file [fraglib_sidechain.mol2] ():/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_sidechain.mol2
| |
| − | ga_torenv_table [fraglib_torenv.dat] ():../ga_calc/unique_full_sorted_fraglib.dat
| |
| − | ga_max_generations [100] ():5
| |
| − | ga_xover_on [yes] (yes no):
| |
| − | ga_xover_sampling_method_rand [yes] (yes no):
| |
| − | ga_xover_max [150] ():
| |
| − | ga_bond_tolerance [0.5] ():
| |
| − | ga_angle_cutoff [0.14] ():
| |
| − | ga_check_overlap [no] (yes no):
| |
| − | ga_mutate_addition [yes] (yes no):
| |
| − | ga_mutate_deletion [yes] (yes no):
| |
| − | ga_mutate_substitution [yes] (yes no):
| |
| − | ga_mutate_replacement [yes] (yes no):
| |
| − | ga_mutate_parents [no] (yes no):yes
| |
| − | ga_pmut_rate [0.3] ():
| |
| − | ga_omut_rate [0.7] ():
| |
| − | ga_max_mut_cycles [5] ():
| |
| − | ga_mut_sampling_method [rand] (rand | graph):
| |
| − | ga_num_random_picks [15] ():
| |
| − | ga_max_root_size [5] ():
| |
| − | ga_energy_cutoff [100] ():
| |
| − | ga_heur_unmatched_num [1] ():
| |
| − | ga_heur_matched_rmsd [0.5] ():
| |
| − | ga_constraint_mol_wt [500] ():
| |
| − | ga_constraint_rot_bon [10] ():
| |
| − | ga_constraint_H_accept [10] ():
| |
| − | ga_constraint_H_don [5] ():
| |
| − | ga_constraint_formal_charge [2] ():
| |
| − | ga_ensemble_size [200] ():100
| |
| − | ga_selection_method [elitism] (elitism | tournament | roulette):
| |
| − | ga_elitism_combined [yes] (yes no):
| |
| − | ga_elitism_option [max] (percent | number | max):
| |
| − | ga_max_num_gen_with_no_crossover [25] ():
| |
| − | ga_name_identifier [ga] ():
| |
| − | ga_output_prefix [ga_output] ():2w26_ga
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy [yes] (yes no):
| |
| − | internal_energy_rep_exp [12] ():
| |
| − | internal_energy_cutoff [100.0] ():
| |
| − | Note: Internal energy only includes repulsive VDW for growth and/or minimization.
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter [no] (yes no):
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand [yes] (yes no):no
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter [no] (yes no):
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules [yes] (yes no):
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary [no] (yes no):
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary [yes] (yes no):no
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | gist_score_primary [no] (yes no):
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | multigrid_score_primary [no] (yes no):
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | dock3.5_score_primary [no] (yes no):
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | continuous_score_primary [no] (yes no):
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | footprint_similarity_score_primary [no] (yes no):
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | pharmacophore_score_primary [no] (yes no):
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | hbond_score_primary [no] (yes no):
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | internal_energy_score_primary [no] (yes no):
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | descriptor_score_primary [no] (yes no):
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | gbsa_zou_score_primary [no] (yes no):
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | gbsa_hawkins_score_primary [no] (yes no):
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | SASA_score_primary [no] (yes no):
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | amber_score_primary [no] (yes no):
| |
| − |
| |
| − | Error: No scoring function selected for the primary score. Program will now terminate.
| |
| − |
| |
| − | (base) [ehspector@milan1 ga_run]$ vi 2w26_ga.in
| |
| − | (base) [ehspector@milan1 ga_run]$ ls
| |
| − | 2w26_ga.in
| |
| − | (base) [ehspector@milan1 ga_run]$ vi 2w26_ga.in
| |
| − | (base) [ehspector@milan1 ga_run]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):genetic
| |
| − |
| |
| − | Genetic Algorithm Recombination Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | ga_molecule_file [ga_molecule_file.mol2] ():^C
| |
| − | (base) [ehspector@milan1 ga_run]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar Robs_2w26
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min ga_calc Robs_new_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore ga_run test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi commands.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ bash commands.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt protein Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd protein/
| |
| − | (base) [ehspector@milan1 protein]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore
| |
| − | 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min
| |
| − | (base) [ehspector@milan1 protein]$ cd ..
| |
| − | (base) [ehspector@milan1 AMS_536]$ rm -r protein/
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi commands.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar Robs_2w26
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min ga_calc Robs_new_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore ga_run test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ ls
| |
| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@milan2 ~]$ cd AMS_536/
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/ga_run/
| |
| − | (base) [ehspector@milan2 ga_run]$ ls
| |
| − | 2w26_ga.in 2w26_ga_lib.in
| |
| − | (base) [ehspector@milan2 ga_run]$ vi 2w26_ga_lib.in
| |
| − | (base) [ehspector@milan2 ga_run]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd Robs_new_2w26/
| |
| − | (base) [ehspector@milan2 Robs_new_2w26]$ cd 007_ga_run1/
| |
| − | (base) [ehspector@milan2 007_ga_run1]$ ls
| |
| − | 2W26_ga.in 2W26_ga.restart0000.mol2 2W26_ga.restart0002.mol2 2W26_ga.restart0004.mol2
| |
| − | 2W26_ga.out 2W26_ga.restart0001.mol2 2W26_ga.restart0003.mol2 2W26_ga.restart0005.mol2
| |
| − | (base) [ehspector@milan2 007_ga_run1]$ vi 2W26_ga.in
| |
| − | (base) [ehspector@milan2 007_ga_run1]$ cd ..
| |
| − | (base) [ehspector@milan2 Robs_new_2w26]$ ls
| |
| − | 000_test 001_structure 002_spheres 003_grid 004_dock 005_analysis 006_ga_lib 007_ga_run1
| |
| − | (base) [ehspector@milan2 Robs_new_2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ga_run/
| |
| − | (base) [ehspector@milan2 ga_run]$ ls
| |
| − | 2w26_ga.in 2w26_ga_lib.in
| |
| − | (base) [ehspector@milan2 ga_run]$ rm 2w26_ga_lib.in
| |
| − | (base) [ehspector@milan2 ga_run]$ vi 2w26_ga.in
| |
| − | (base) [ehspector@milan2 ga_run]$ rm 2w26_ga.in
| |
| − | (base) [ehspector@milan2 ga_run]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cp Robs_new_2w26/007_ga_run1/2W26_ga.in ga_calc/2w26_ga.in
| |
| − | (base) [ehspector@milan2 2w26]$ mv ga_calc/2w26_ga.in ga_run/
| |
| − | (base) [ehspector@milan2 2w26]$ mv ga_run/ ga_run_5
| |
| − | (base) [ehspector@milan2 2w26]$ mkdir ga_run_50
| |
| − | (base) [ehspector@milan2 2w26]$ cd ga_run_5
| |
| − | (base) [ehspector@milan2 ga_run_5]$ ls
| |
| − | 2w26_ga.in
| |
| − | (base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.in
| |
| − | (base) [ehspector@milan2 ga_run_5]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in -o 2w26_ga.out
| |
| − | (base) [ehspector@milan2 ga_run_5]$ ls
| |
| − | 2w26_ga.in 2w26_ga.out
| |
| − | (base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.out
| |
| − | (base) [ehspector@milan2 ga_run_5]$ vi 2w26_ga.in
| |
| − | (base) [ehspector@milan2 ga_run_5]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i 2w26_ga.in -o 2w26_ga.out
| |
| − | (base) [ehspector@milan2 ga_run_5]$ ls
| |
| − | 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0004.mol2 2w26_ga.in
| |
| − | 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0005.mol2 2w26_ga.out
| |
| − | (base) [ehspector@milan2 ga_run_5]$ mv 2w26_ga.in 2w26_ga_5.in
| |
| − | (base) [ehspector@milan2 ga_run_5]$ mv 2w26_ga.out 2w26_ga_5.out
| |
| − | (base) [ehspector@milan2 ga_run_5]$ ls
| |
| − | 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0004.mol2 2w26_ga_5.in
| |
| − | 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0005.mol2 2w26_ga_5.out
| |
| − | (base) [ehspector@milan2 ga_run_5]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cp ga_run_5/2w26_ga_5.in ga_run_50/2w26_ga_50.in
| |
| − | (base) [ehspector@milan2 2w26]$ cp 007_virtual_screen/virtual.sh ga_run_50/ga.sh
| |
| − | (base) [ehspector@milan2 2w26]$ cd ga_run_50
| |
| − | (base) [ehspector@milan2 ga_run_50]$ ls
| |
| − | 2w26_ga_50.in ga.sh
| |
| − | (base) [ehspector@milan2 ga_run_50]$ vi ga.sh
| |
| − | (base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in
| |
| − | (base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in
| |
| − | (base) [ehspector@milan2 ga_run_50]$ vi 2w26_ga_50.in
| |
| − | (base) [ehspector@milan2 ga_run_50]$ avail
| |
| − | PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
| |
| − | a100 up 8:00:00 2 mix@ a100-[02,04]
| |
| − | a100 up 8:00:00 8 alloc@ a100-[03,05-11]
| |
| − | a100 up 8:00:00 1 drain* a100-01
| |
| − | a100-large up 8:00:00 2 mix@ a100-[02,04]
| |
| − | a100-large up 8:00:00 8 alloc@ a100-[03,05-11]
| |
| − | a100-large up 8:00:00 1 drain* a100-01
| |
| − | a100-long up 2-00:00:00 2 mix@ a100-[02,04]
| |
| − | a100-long up 2-00:00:00 8 alloc@ a100-[03,05-11]
| |
| − | a100-long up 2-00:00:00 1 drain* a100-01
| |
| − | debug-40core up 1:00:00 2 drain* dn[031,037]
| |
| − | debug-40core up 1:00:00 1 drain dn061
| |
| − | debug-40core up 1:00:00 10 mix dn[020-021,041-043,052-053,056,059-060]
| |
| − | debug-40core up 1:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
| |
| − | extended-40core up 7-00:00:00 2 drain* dn[031,037]
| |
| − | extended-40core up 7-00:00:00 1 drain dn061
| |
| − | extended-40core up 7-00:00:00 10 mix dn[020-021,041-043,052-053,056,059-060]
| |
| − | extended-40core up 7-00:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
| |
| − | extended-40core-shared up 3-12:00:00 2 drain* dn[031,037]
| |
| − | extended-40core-shared up 3-12:00:00 1 drain dn061
| |
| − | extended-40core-shared up 3-12:00:00 10 mix dn[020-021,041-043,052-053,056,059-060]
| |
| − | extended-40core-shared up 3-12:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
| |
| − | extended-96core up 7-00:00:00 1 plnd dg025
| |
| − | extended-96core up 7-00:00:00 1 drng@ dg023
| |
| − | extended-96core up 7-00:00:00 1 mix@ dg039
| |
| − | extended-96core up 7-00:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040]
| |
| − | extended-96core up 7-00:00:00 1 down* dg009
| |
| − | extended-96core up 7-00:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
| |
| − | extended-96core-shared up 3-12:00:00 1 plnd dg025
| |
| − | extended-96core-shared up 3-12:00:00 1 drng@ dg023
| |
| − | extended-96core-shared up 3-12:00:00 1 mix@ dg039
| |
| − | extended-96core-shared up 3-12:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040]
| |
| − | extended-96core-shared up 3-12:00:00 1 down* dg009
| |
| − | extended-96core-shared up 3-12:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 3 alloc xm[046-048]
| |
| − | hbm-1tb-long-96core up 2-00:00:00 1 idle xm045
| |
| − | hbm-extended-96core up 7-00:00:00 3 plnd xm[008,021,088]
| |
| − | hbm-extended-96core up 7-00:00:00 9 alloc@ xm[016,019,028-029,031,037,054,081-082]
| |
| − | hbm-extended-96core up 7-00:00:00 78 alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
| |
| − | hbm-large-96core up 8:00:00 3 plnd xm[008,021,088]
| |
| − | hbm-large-96core up 8:00:00 9 alloc@ xm[016,019,028-029,031,037,054,081-082]
| |
| − | hbm-large-96core up 8:00:00 78 alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
| |
| − | hbm-long-96core up 2-00:00:00 3 plnd xm[008,021,088]
| |
| − | hbm-long-96core up 2-00:00:00 9 alloc@ xm[016,019,028-029,031,037,054,081-082]
| |
| − | hbm-long-96core up 2-00:00:00 78 alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
| |
| − | hbm-medium-96core up 12:00:00 3 plnd xm[008,021,088]
| |
| − | hbm-medium-96core up 12:00:00 9 alloc@ xm[016,019,028-029,031,037,054,081-082]
| |
| − | hbm-medium-96core up 12:00:00 78 alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
| |
| − | hbm-short-96core up 4:00:00 3 plnd xm[008,021,088]
| |
| − | hbm-short-96core up 4:00:00 9 alloc@ xm[016,019,028-029,031,037,054,081-082]
| |
| − | hbm-short-96core up 4:00:00 78 alloc xm[001-007,009-015,017-018,020,022-027,030,032-036,038-044,049-053,055-080,083-087,089-094]
| |
| − | large-40core up 8:00:00 2 drain* dn[031,037]
| |
| − | large-40core up 8:00:00 1 drain dn061
| |
| − | large-40core up 8:00:00 10 mix dn[020-021,041-043,052-053,056,059-060]
| |
| − | large-40core up 8:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
| |
| − | large-96core up 8:00:00 1 plnd dg025
| |
| − | large-96core up 8:00:00 1 drng@ dg023
| |
| − | large-96core up 8:00:00 1 mix@ dg039
| |
| − | large-96core up 8:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040]
| |
| − | large-96core up 8:00:00 1 down* dg009
| |
| − | large-96core up 8:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
| |
| − | long-40core up 2-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core up 2-00:00:00 1 drain dn061
| |
| − | long-40core up 2-00:00:00 10 mix dn[020-021,041-043,052-053,056,059-060]
| |
| − | long-40core up 2-00:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
| |
| − | long-40core-shared up 1-00:00:00 2 drain* dn[031,037]
| |
| − | long-40core-shared up 1-00:00:00 1 drain dn061
| |
| − | long-40core-shared up 1-00:00:00 10 mix dn[020-021,041-043,052-053,056,059-060]
| |
| − | long-40core-shared up 1-00:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
| |
| − | long-96core up 2-00:00:00 1 plnd dg025
| |
| − | long-96core up 2-00:00:00 1 drng@ dg023
| |
| − | long-96core up 2-00:00:00 1 mix@ dg039
| |
| − | long-96core up 2-00:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040]
| |
| − | long-96core up 2-00:00:00 1 down* dg009
| |
| − | long-96core up 2-00:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
| |
| − | long-96core-shared up 1-00:00:00 1 plnd dg025
| |
| − | long-96core-shared up 1-00:00:00 1 drng@ dg023
| |
| − | long-96core-shared up 1-00:00:00 1 mix@ dg039
| |
| − | long-96core-shared up 1-00:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040]
| |
| − | long-96core-shared up 1-00:00:00 1 down* dg009
| |
| − | long-96core-shared up 1-00:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
| |
| − | medium-40core up 12:00:00 2 drain* dn[031,037]
| |
| − | medium-40core up 12:00:00 1 drain dn061
| |
| − | medium-40core up 12:00:00 10 mix dn[020-021,041-043,052-053,056,059-060]
| |
| − | medium-40core up 12:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
| |
| − | medium-96core up 12:00:00 1 plnd dg025
| |
| − | medium-96core up 12:00:00 1 drng@ dg023
| |
| − | medium-96core up 12:00:00 1 mix@ dg039
| |
| − | medium-96core up 12:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040]
| |
| − | medium-96core up 12:00:00 1 down* dg009
| |
| − | medium-96core up 12:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
| |
| − | ood-short-96core up 4:00:00 1 idle dg038
| |
| − | rn-long-40core up 8-08:00:00 12 idle rn[001-012]
| |
| − | short-40core up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core up 4:00:00 1 drain dn061
| |
| − | short-40core up 4:00:00 10 mix dn[020-021,041-043,052-053,056,059-060]
| |
| − | short-40core up 4:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
| |
| − | short-40core-shared up 4:00:00 2 drain* dn[031,037]
| |
| − | short-40core-shared up 4:00:00 1 drain dn061
| |
| − | short-40core-shared up 4:00:00 10 mix dn[020-021,041-043,052-053,056,059-060]
| |
| − | short-40core-shared up 4:00:00 49 alloc dn[001-019,022-030,032-036,038-040,044-051,054-055,057-058,062]
| |
| − | short-96core up 4:00:00 1 plnd dg025
| |
| − | short-96core up 4:00:00 1 drng@ dg023
| |
| − | short-96core up 4:00:00 1 mix@ dg039
| |
| − | short-96core up 4:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040]
| |
| − | short-96core up 4:00:00 1 down* dg009
| |
| − | short-96core up 4:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
| |
| − | short-96core-shared up 4:00:00 1 plnd dg025
| |
| − | short-96core-shared up 4:00:00 1 drng@ dg023
| |
| − | short-96core-shared up 4:00:00 1 mix@ dg039
| |
| − | short-96core-shared up 4:00:00 8 alloc@ dg[006,010-011,014-015,019,030,040]
| |
| − | short-96core-shared up 4:00:00 1 down* dg009
| |
| − | short-96core-shared up 4:00:00 35 alloc dg[001-005,007-008,012-013,016-018,020-022,024,026-029,031-037,041-048]
| |
| − | (base) [ehspector@milan2 ga_run_50]$ vi ga.sh
| |
| − |
| |
| − |
| |
| − | Press ENTER or type command to continue
| |
| − | (base) [ehspector@milan2 ga_run_50]$ ls
| |
| − | 2w26_ga_50.in ga.sh
| |
| − | (base) [ehspector@milan2 ga_run_50]$ vi ga.sh
| |
| − | (base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh
| |
| − | Submitted batch job 932640
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932640 short-96c 2w26_ga_ ehspecto PD 0:00 3 (Resources)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932640 short-96c 2w26_ga_ ehspecto PD 0:00 3 (Resources)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932640 short-96c 2w26_ga_ ehspecto PD 0:00 3 (Resources)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932640 short-96c 2w26_ga_ ehspecto PD 0:00 3 (Resources)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932640 short-96c 2w26_ga_ ehspecto PD 0:00 3 (Resources)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ ^C
| |
| − | (base) [ehspector@milan2 ga_run_50]$ vi ga.sh
| |
| − | (base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh
| |
| − | Submitted batch job 932642
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932642 ood-short 2w26_ga_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 932640 short-96c 2w26_ga_ ehspecto PD 0:00 3 (Resources)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932642 ood-short 2w26_ga_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 932640 short-96c 2w26_ga_ ehspecto PD 0:00 3 (Resources)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932642 ood-short 2w26_ga_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 932640 short-96c 2w26_ga_ ehspecto PD 0:00 3 (Resources)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932642 ood-short 2w26_ga_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 932640 short-96c 2w26_ga_ ehspecto PD 0:00 3 (Resources)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932642 ood-short 2w26_ga_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 932640 short-96c 2w26_ga_ ehspecto PD 0:00 3 (Resources)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932642 ood-short 2w26_ga_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | 932640 short-96c 2w26_ga_ ehspecto PD 0:00 3 (Resources)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ scancel 932640
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932642 ood-short 2w26_ga_ ehspecto PD 0:00 3 (PartitionNodeLimit)
| |
| − | (base) [ehspector@milan2 ga_run_50]$ scancel 932642
| |
| − | (base) [ehspector@milan2 ga_run_50]$ ls
| |
| − | 2w26_ga_50.in ga.sh
| |
| − | (base) [ehspector@milan2 ga_run_50]$ vi ga.sh
| |
| − | (base) [ehspector@milan2 ga_run_50]$ sbatch ga.sh
| |
| − | Submitted batch job 932644
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932644 ood-short 2w26_ga_ ehspecto R 0:03 1 dg038
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932644 ood-short 2w26_ga_ ehspecto R 0:07 1 dg038
| |
| − | (base) [ehspector@milan2 ga_run_50]$ ls
| |
| − | 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0003.mol2 2w26_ga_50.in vs_output.txt
| |
| − | 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0004.mol2 2w26_ga_50.out
| |
| − | 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0005.mol2 ga.sh
| |
| − | (base) [ehspector@milan2 ga_run_50]$ ls
| |
| − | 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0006.mol2 ga.sh
| |
| − | 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0004.mol2 2w26_ga_50.in vs_output.txt
| |
| − | 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0005.mol2 2w26_ga_50.out
| |
| − | (base) [ehspector@milan2 ga_run_50]$ ls
| |
| − | 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0006.mol2 ga.sh
| |
| − | 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0004.mol2 2w26_ga_50.in vs_output.txt
| |
| − | 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0005.mol2 2w26_ga_50.out
| |
| − | (base) [ehspector@milan2 ga_run_50]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932644 ood-short 2w26_ga_ ehspecto R 0:41 1 dg038
| |
| − | (base) [ehspector@milan2 ga_run_50]$ exit
| |
| − | logout
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ vi Notes.txt
| |
| − | (base) [ehspector@milan2 AMS_536]$ check
| |
| − | JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| |
| − | 932644 ood-short 2w26_ga_ ehspecto R 8:17 1 dg038
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar ga_run_50 test4.tar
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min ga_calc Robs_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore ga_run_5 Robs_new_2w26
| |
| − | (base) [ehspector@milan2 2w26]$ cd ga_run_50/
| |
| − | (base) [ehspector@milan2 ga_run_50]$ ls
| |
| − | 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0008.mol2 2w26_5_ga.restart0016.mol2
| |
| − | 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0009.mol2 2w26_5_ga.restart0017.mol2
| |
| − | 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0010.mol2 2w26_5_ga.restart0018.mol2
| |
| − | 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0011.mol2 2w26_ga_50.in
| |
| − | 2w26_5_ga.restart0004.mol2 2w26_5_ga.restart0012.mol2 2w26_ga_50.out
| |
| − | 2w26_5_ga.restart0005.mol2 2w26_5_ga.restart0013.mol2 ga.sh
| |
| − | 2w26_5_ga.restart0006.mol2 2w26_5_ga.restart0014.mol2 vs_output.txt
| |
| − | 2w26_5_ga.restart0007.mol2 2w26_5_ga.restart0015.mol2
| |
| − | (base) [ehspector@milan2 ga_run_50]$ exit
| |
| − | logout
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ ls
| |
| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@milan2 ~]$ cd AMS_536/
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/2w26/ga_run_50/
| |
| − | (base) [ehspector@milan2 ga_run_50]$ ls
| |
| − | 2w26_5_ga.restart0000.mol2 2w26_5_ga.restart0019.mol2 2w26_5_ga.restart0038.mol2
| |
| − | 2w26_5_ga.restart0001.mol2 2w26_5_ga.restart0020.mol2 2w26_5_ga.restart0039.mol2
| |
| − | 2w26_5_ga.restart0002.mol2 2w26_5_ga.restart0021.mol2 2w26_5_ga.restart0040.mol2
| |
| − | 2w26_5_ga.restart0003.mol2 2w26_5_ga.restart0022.mol2 2w26_5_ga.restart0041.mol2
| |
| − | 2w26_5_ga.restart0004.mol2 2w26_5_ga.restart0023.mol2 2w26_5_ga.restart0042.mol2
| |
| − | 2w26_5_ga.restart0005.mol2 2w26_5_ga.restart0024.mol2 2w26_5_ga.restart0043.mol2
| |
| − | 2w26_5_ga.restart0006.mol2 2w26_5_ga.restart0025.mol2 2w26_5_ga.restart0044.mol2
| |
| − | 2w26_5_ga.restart0007.mol2 2w26_5_ga.restart0026.mol2 2w26_5_ga.restart0045.mol2
| |
| − | 2w26_5_ga.restart0008.mol2 2w26_5_ga.restart0027.mol2 2w26_5_ga.restart0046.mol2
| |
| − | 2w26_5_ga.restart0009.mol2 2w26_5_ga.restart0028.mol2 2w26_5_ga.restart0047.mol2
| |
| − | 2w26_5_ga.restart0010.mol2 2w26_5_ga.restart0029.mol2 2w26_5_ga.restart0048.mol2
| |
| − | 2w26_5_ga.restart0011.mol2 2w26_5_ga.restart0030.mol2 2w26_5_ga.restart0049.mol2
| |
| − | 2w26_5_ga.restart0012.mol2 2w26_5_ga.restart0031.mol2 2w26_5_ga.restart0050.mol2
| |
| − | 2w26_5_ga.restart0013.mol2 2w26_5_ga.restart0032.mol2 2w26_ga_50.in
| |
| − | 2w26_5_ga.restart0014.mol2 2w26_5_ga.restart0033.mol2 2w26_ga_50.out
| |
| − | 2w26_5_ga.restart0015.mol2 2w26_5_ga.restart0034.mol2 ga.sh
| |
| − | 2w26_5_ga.restart0016.mol2 2w26_5_ga.restart0035.mol2 vs_output.txt
| |
| − | 2w26_5_ga.restart0017.mol2 2w26_5_ga.restart0036.mol2
| |
| − | 2w26_5_ga.restart0018.mol2 2w26_5_ga.restart0037.mol2
| |
| − | (base) [ehspector@milan2 ga_run_50]$ mkdir 50_generations
| |
| − | (base) [ehspector@milan2 ga_run_50]$ mv *.mol2 50_generations/
| |
| − | (base) [ehspector@milan2 ga_run_50]$ ls
| |
| − | 2w26_ga_50.in 2w26_ga_50.out 50_generations ga.sh vs_output.txt
| |
| − | (base) [ehspector@milan2 ga_run_50]$ cd 50_generations/
| |
| − | (base) [ehspector@milan2 50_generations]$ cd ..
| |
| − | (base) [ehspector@milan2 ga_run_50]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ga_run_5
| |
| − | (base) [ehspector@milan2 ga_run_5]$ mkdir 5_generations
| |
| − | (base) [ehspector@milan2 ga_run_5]$ mv *.mol2 5_generations/
| |
| − | (base) [ehspector@milan2 ga_run_5]$ ls
| |
| − | 2w26_ga_5.in 2w26_ga_5.out 5_generations
| |
| − | (base) [ehspector@milan2 ga_run_5]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tut(base) [ehspect(base) [ehspector@m(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 (base) [ehspector@milan2 Tutorials]$ (base) [ehspector@milan(base) [(base) [ehspector@mila(base) [e(base) [ehspector@milan2 Tutori(base) [ehspector@milan2 Tutorials]$ client_loop: send disconnect: Broken pipe
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ home
| |
| − | (base) [ehspector@milan1 espector]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 004_energymin 007_virtual_screen 2025_02_12a_test.tar ga_run_50 test4.tar
| |
| − | 002_surface_spheres 005_dock 008_cartesian_min ga_calc Robs_2w26
| |
| − | 003_gridbox 006_footprint 009_rescore ga_run_5 Robs_new_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cd ga_calc/
| |
| − | (base) [ehspector@milan1 ga_calc]$ ls
| |
| − | 2w26_fraglib.in 2w26_fraglib_scored.mol2 lib.sh
| |
| − | 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 py.sh
| |
| − | 2w26_fraglib.out 2W26_fraglib_torenv.dat unique_full_sorted_fraglib.dat
| |
| − | 2W26_fraglib_rigid.mol2 full_fraglib.dat
| |
| − | 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat
| |
| − | (base) [ehspector@milan1 ga_calc]$ vi py.sh
| |
| − | (base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base) [ehspector@milan1 ga_ca(base(base) [ehspector@milan1 ga_c(base) [ehspector@milan1 ga_calc]$ ls
| |
| − | 2w26_fraglib.in 2w26_fraglib_scored.mol2 lib.sh
| |
| − | 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 py.sh
| |
| − | 2w26_fraglib.out 2W26_fraglib_torenv.dat unique_full_sorted_fraglib.dat
| |
| − | 2W26_fraglib_rigid.mol2 full_fraglib.dat
| |
| − | 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat
| |
| − | (base) [ehspector@milan1 ga_calc]$ ls
| |
| − | 2w26_fraglib.in 2w26_fraglib_scored.mol2 lib.sh
| |
| − | 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 py.sh
| |
| − | 2w26_fraglib.out 2W26_fraglib_torenv.dat unique_full_sorted_fraglib.dat
| |
| − | 2W26_fraglib_rigid.mol2 full_fraglib.dat
| |
| − | 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat
| |
| − | (base) [ehspector@milan1 ga_calc]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 005_dock 009_rescore ga_run_50
| |
| − | 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26
| |
| − | 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26
| |
| − | 004_energymin 008_cartesian_min ga_run_5 test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 005_dock 009_rescore ga_run_50
| |
| − | 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26
| |
| − | 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26
| |
| − | 004_energymin 008_cartesian_min ga_run_5 test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 005_dock 009_rescore ga_run_50
| |
| − | 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26
| |
| − | 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26
| |
| − | 004_energymin 008_cartesian_min ga_run_5 test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 005_dock 009_rescore ga_run_50
| |
| − | 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26
| |
| − | 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26
| |
| − | 004_energymin 008_cartesian_min ga_run_5 test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ cd ga_run_5
| |
| − | (base) [ehspector@milan1 ga_run_5]$ cd ..
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 005_dock 009_rescore ga_run_50
| |
| − | 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26
| |
| − | 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26
| |
| − | 004_energymin 008_cartesian_min ga_run_5 test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi commands.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 005_dock 009_rescore ga_run_50
| |
| − | 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26
| |
| − | 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26
| |
| − | 004_energymin 008_cartesian_min ga_run_5 test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 005_dock 009_rescore ga_run_50
| |
| − | 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26
| |
| − | 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26
| |
| − | 004_energymin 008_cartesian_min ga_run_5 test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ cd ..
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ cd ../../
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd ../../
| |
| − | (base) [ehspector@milan1 ~]$ ls
| |
| − | AMS_536 miniconda3 Miniconda3-latest-Linux-x86_64.sh
| |
| − | (base) [ehspector@milan1 ~]$ cd AMS_536/
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd ../
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi commands.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ touch make_folders
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi make_folders
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt make_folders Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ bash make_folders
| |
| − | make_folders: line 3: folder: Is a directory
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt folder make_folders Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd folder/
| |
| − | (base) [ehspector@milan1 folder]$ ls
| |
| − | (base) [ehspector@milan1 folder]$ cd ..
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt folder make_folders Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ rm -r folder/
| |
| − | (base) [ehspector@milan1 AMS_536]$ rm make_folders
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd ..
| |
| − | (base) [ehspector@milan1 ~]$ cd AMS_536/
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd ..
| |
| − | (base) [ehspector@milan1 ~]$ cd ..
| |
| − | (base) [ehspector@milan1 home]$ cd ..
| |
| − | (base) [ehspector@milan1 gpfs]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
| |
| − | (base) [ehspector@milan1 bin]$ ls
| |
| − | am1bcc dock6.mpi multigrid_fp_gen.py sevsolv
| |
| − | amberize_complex espgen nchemgrid_GB showbox
| |
| − | amberize_ligand grid nchemgrid_SA showsphere
| |
| − | amberize_receptor grid-convert parmcal solvgrid
| |
| − | antechamber grid-convrds parmchk solvmap
| |
| − | atomtype make_phimap prepare_amber.pl sphere_selector
| |
| − | bondtype mol2bild.py prepare_rna_amber.pl sphgen
| |
| − | chemgrid mol2.py prepgen teLeap
| |
| − | combine_torenv.py mopac resp tleap
| |
| − | dock6 mopac.sh respgen
| |
| − | (base) [ehspector@milan1 bin]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 005_dock 009_rescore ga_run_50
| |
| − | 002_surface_spheres 006_footprint 2025_02_12a_test.tar Robs_2w26
| |
| − | 003_gridbox 007_virtual_screen ga_calc Robs_new_2w26
| |
| − | 004_energymin 008_cartesian_min ga_run_5 test4.tar
| |
| − | (base) [ehspector@milan1 2w26]$ mkdir de_novo
| |
| − | (base) [ehspector@milan1 2w26]$ ls
| |
| − | 001_structure 005_dock 009_rescore ga_run_5 test4.tar
| |
| − | 002_surface_spheres 006_footprint 2025_02_12a_test.tar ga_run_50
| |
| − | 003_gridbox 007_virtual_screen de_novo Robs_2w26
| |
| − | 004_energymin 008_cartesian_min ga_calc Robs_new_2w26
| |
| − | (base) [ehspector@milan1 2w26]$ cd ../../
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi Notes.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi Notes.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
| |
| − | -bash: cd: projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
| |
| − | -bash: cd: projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/
| |
| − | -bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/
| |
| − | -bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/: No such file or directory
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
| |
| − | -bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin: No such file or directory
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd
| |
| − | (base) [ehspector@milan1 ~]$ cd gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin
| |
| − | -bash: cd: gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin: No such file or directory
| |
| − | (base) [ehspector@milan1 ~]$ cd ..
| |
| − | (base) [ehspector@milan1 home]$ cd ..
| |
| − | (base) [ehspector@milan1 gpfs]$ cd projects/AMS536/zzz.programs/dock6.12_ams536/bin/
| |
| − | (base) [ehspector@milan1 bin]$ ls
| |
| − | am1bcc dock6.mpi multigrid_fp_gen.py sevsolv
| |
| − | amberize_complex espgen nchemgrid_GB showbox
| |
| − | amberize_ligand grid nchemgrid_SA showsphere
| |
| − | amberize_receptor grid-convert parmcal solvgrid
| |
| − | antechamber grid-convrds parmchk solvmap
| |
| − | atomtype make_phimap prepare_amber.pl sphere_selector
| |
| − | bondtype mol2bild.py prepare_rna_amber.pl sphgen
| |
| − | chemgrid mol2.py prepgen teLeap
| |
| − | combine_torenv.py mopac resp tleap
| |
| − | dock6 mopac.sh respgen
| |
| − | (base) [ehspector@milan1 bin]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/tleap
| |
| − | /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/tleap
| |
| − | (base) [ehspector@milan1 bin]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd ..
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi Notes.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ top
| |
| − |
| |
| − | top - 15:15:15 up 1 day, 2:11, 24 users, load average: 0.72, 1.86, 3.46
| |
| − | Tasks: 1532 total, 2 running, 1530 sleeping, 0 stopped, 0 zombie
| |
| − | %Cpu(s): 0.8 us, 0.0 sy, 0.0 ni, 99.2 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
| |
| − | MiB Mem : 515564.8 total, 495571.2 free, 20722.4 used, 2594.1 buff/cache
| |
| − | MiB Swap: 0.0 total, 0.0 free, 0.0 used. 494842.4 avail Mem
| |
| − |
| |
| − | PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
| |
| − | 339567 minkwan 20 0 164580 90868 3072 R 99.0 0.0 0:25.66 dock6
| |
| − | 339594 ehspect+ 20 0 23432 4096 3072 R 1.6 0.0 0:00.30 top
| |
| − | 4135 root 20 0 259340 20196 16384 S 1.0 0.0 4:53.58 NetworkManager
| |
| − | 276537 eswong 20 0 295692 13164 5120 S 0.5 0.0 0:11.35 code-e54c774e0a
| |
| − | 335183 hborche+ 20 0 4280208 284596 82944 S 0.5 0.1 0:01.07 cpptools-srv
| |
| − | 1 root 20 0 172980 12288 9216 S 0.0 0.0 0:40.57 systemd
| |
| − | 2 root 20 0 0 0 0 S 0.0 0.0 0:00.25 kthreadd
| |
| − | 3 root 0 -20 0 0 0 I 0.0 0.0 0:00.00 rcu_gp
| |
| − | 4 root 0 -20 0 0 0 I 0.0 0.0 0:00.00 rcu_par_gp
| |
| − | 5 root 0 -20 0 0 0 I 0.0 0.0 0:00.00 slub_flushwq
| |
| − | 6 root 0 -20 0 0 0 I 0.0 0.0 0:00.00 netns
| |
| − | 8 root 0 -20 0 0 0 I 0.0 0.0 0:00.00 kworker/0:0H-events+
| |
| − | 12 root 0 -20 0 0 0 I 0.0 0.0 0:00.00 mm_percpu_wq
| |
| − | 13 root 20 0 0 0 0 I 0.0 0.0 0:00.00 rcu_tasks_kthre
| |
| − | 14 root 20 0 0 0 0 I 0.0 0.0 0:00.00 rcu_tasks_rude_
| |
| − | 15 root 20 0 0 0 0 I 0.0 0.0 0:00.00 rcu_tasks_trace
| |
| − | 16 root 20 0 0 0 0 S 0.0 0.0 0:00.38 ksoftirqd/0
| |
| − | 17 root 20 0 0 0 0 I 0.0 0.0 0:50.41 rcu_preempt
| |
| − | 18 root rt 0 0 0 0 S 0.0 0.0 0:00.08 migration/0
| |
| − | 20 root -51 0 0 0 0 S 0.0 0.0 0:00.00 idle_inject/0
| |
| − | 21 root 20 0 0 0 0 S 0.0 0.0 0:00.00 cpuhp/0
| |
| − | 22 root 20 0 0 0 0 S 0.0 0.0 0:00.00 cpuhp/1
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd ..
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan1 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ls
| |
| − | 1O86 2w26 5EEN folders.txt
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Permission denied, please try again.
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ vi Notes.txt
| |
| − | (base) [ehspector@milan1 AMS_536]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ vi ~/.bashrc
| |
| − | (base) [ehspector@milan1 ~]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ~]$ home
| |
| − | (base) [ehspector@milan2 espector]$ ls
| |
| − | 25K 4s0v builds gas_test RDKit segfault_test_2 sphere_test
| |
| − | (base) [ehspector@milan2 espector]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/
| |
| − | (base) [ehspector@milan2 2w26]$ ls
| |
| − | 001_structure 005_dock 009_rescore ga_run_5 test4.tar
| |
| − | 002_surface_spheres 006_footprint 2025_02_12a_test.tar ga_run_50
| |
| − | 003_gridbox 007_virtual_screen de_novo Robs_2w26
| |
| − | 004_energymin 008_cartesian_min ga_calc Robs_new_2w26
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/
| |
| − | (base) [ehspector@milan2 1O86]$ mkdir de_novo
| |
| − | (base) [ehspector@milan2 1O86]$ cd de_novo/
| |
| − | (base) [ehspector@milan2 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2
| |
| − | (base) [ehspector@milan2 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2
| |
| − | (base) [ehspector@milan2 de_novo]$ touch Du.in
| |
| − | (base) [ehspector@milan2 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2 Du.in
| |
| − | (base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in
| |
| − |
| |
| − |
| |
| − |
| |
| − | --------------------------------------
| |
| − | DOCK v6.12
| |
| − |
| |
| − | Released September 2024
| |
| − | Copyright UCSF
| |
| − | --------------------------------------
| |
| − |
| |
| − |
| |
| − | Conformational Sampling Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | conformer_search_type [flex] (rigid | flex | denovo | covalent | genetic | HDB):denovo
| |
| − |
| |
| − | De Novo Build Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | dn_fraglib_scaffold_file [fraglib_scaffold.mol2] ():
| |
| − | dn_fraglib_linker_file [fraglib_linker.mol2] ():
| |
| − | dn_fraglib_sidechain_file [fraglib_sidechain.mol2] ():
| |
| − | dn_user_specified_anchor [yes] (yes no):
| |
| − | dn_fraglib_anchor_file [fraglib_anchor.mol2] ():
| |
| − | dn_torenv_table [fraglib_torenv.dat] ():
| |
| − | dn_name_identifier [denovo] ():
| |
| − | dn_sampling_method [graph] (ex | rand | graph):
| |
| − | dn_graph_max_picks [30] ():
| |
| − | dn_graph_breadth [3] ():
| |
| − | dn_graph_depth [2] ():
| |
| − | dn_graph_temperature [100.0] ():
| |
| − | dn_pruning_conformer_score_cutoff [100.0] ():
| |
| − | dn_pruning_conformer_score_scaling_factor [2.0] ():
| |
| − | dn_pruning_clustering_cutoff [100.0] ():
| |
| − | dn_remove_duplicates [yes] ( no | yes):
| |
| − | dn_max_duplicates_per_mol [0] ():
| |
| − | dn_write_pruned_duplicates [no] ( no | yes ):
| |
| − | dn_advanced_pruning [yes] (yes | no):
| |
| − | dn_prune_initial_sample [yes] (yes | no):
| |
| − | dn_sample_torsions [yes] (yes | no):
| |
| − | dn_prune_individual_torsions [yes] (yes | no):
| |
| − | dn_prune_combined_torsions [yes] (yes | no):
| |
| − | dn_random_root_selection [no] (yes | no):
| |
| − | dn_mol_wt_cutoff_type [soft] (hard | soft):
| |
| − | dn_upper_constraint_mol_wt [550.0] ():500
| |
| − | dn_lower_constraint_mol_wt [0.0] ():
| |
| − | dn_mol_wt_std_dev [35.0] ():
| |
| − | dn_constraint_rot_bon [15] ():
| |
| − | dn_constraint_formal_charge [2.0] ():
| |
| − | dn_heur_unmatched_num [1] ():
| |
| − | dn_heur_matched_rmsd [2.0] ():
| |
| − | dn_unique_anchors [1] ():
| |
| − | dn_max_grow_layers [9] ():
| |
| − | dn_max_root_size [25] ():
| |
| − | dn_max_layer_size [25] ():
| |
| − | dn_max_current_aps [5] ():
| |
| − | dn_max_scaffolds_per_layer [1] ():
| |
| − | dn_max_successful_att_per_root [50000] ():
| |
| − | dn_write_checkpoints [yes] (yes no):
| |
| − | dn_write_prune_dump [yes] (yes no):
| |
| − | dn_write_orients [no] (yes no):
| |
| − | dn_write_growth_trees [no] (yes no):
| |
| − | dn_output_prefix [output] ():
| |
| − |
| |
| − | Internal Energy Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_internal_energy [yes] (yes no):
| |
| − | internal_energy_rep_exp [12] ():
| |
| − | internal_energy_cutoff [100.0] ():
| |
| − | Note: Internal energy only includes repulsive VDW for growth and/or minimization.
| |
| − |
| |
| − | Database Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | use_database_filter [no] (yes no):
| |
| − |
| |
| − | Orient Ligand Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | orient_ligand [yes] (yes no):no
| |
| − |
| |
| − | Bump Filter Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | bump_filter [no] (yes no):
| |
| − |
| |
| − | Master Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | score_molecules [yes] (yes no):
| |
| − |
| |
| − | Contact Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | contact_score_primary [no] (yes no):
| |
| − |
| |
| − | Grid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | grid_score_primary [yes] (yes no):
| |
| − | grid_score_rep_rad_scale [1] ():
| |
| − | grid_score_vdw_scale [1] ():
| |
| − | grid_score_es_scale [1] ():
| |
| − | grid_lig_efficiency [no] (yes no):
| |
| − | grid_score_grid_prefix [grid] ():
| |
| − |
| |
| − | GIST Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | MultiGrid Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Dock3.5 Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Continuous Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Footprint Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Pharmacophore Similarity Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hbond Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Internal Energy Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Descriptor Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Zou GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Hawkins GB/SA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | SASA Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Amber Score Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Simplex Minimization Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | minimize_ligand [yes] (yes no):
| |
| − | minimize_anchor [yes] (yes no):
| |
| − | minimize_flexible_growth [yes] (yes no):
| |
| − | use_advanced_simplex_parameters [no] (yes no):
| |
| − | simplex_max_cycles [1] ():
| |
| − | simplex_score_converge [0.1] ():
| |
| − | simplex_cycle_converge [1.0] ():
| |
| − | simplex_trans_step [1.0] ():
| |
| − | simplex_rot_step [0.1] ():
| |
| − | simplex_tors_step [10.0] ():
| |
| − | simplex_anchor_max_iterations [500] ():
| |
| − | simplex_grow_max_iterations [500] ():
| |
| − | simplex_grow_tors_premin_iterations [0] ():
| |
| − | simplex_final_min [no] (yes no):
| |
| − | simplex_random_seed [0] ():
| |
| − | simplex_restraint_min [no] (yes no):
| |
| − |
| |
| − | Atom Typing Parameters
| |
| − | ------------------------------------------------------------------------------------------
| |
| − | atom_model [all] (all | united):
| |
| − | vdw_defn_file [vdw.defn] ():
| |
| − | flex_defn_file [flex.defn] ():
| |
| − | flex_drive_file [flex_drive.tbl] ():
| |
| − | ------------------------------------------------------------------------------------------
| |
| − |
| |
| − | Initializing De Novo Growth Routines...
| |
| − | Reading the scaffold library from fraglib_scaffold.mol2...Could not open fraglib_scaffold.mol2. Program will terminate.
| |
| − | No such file or directory(base) [ehspector@milan2 de_novo]$ vi Du.in
| |
| − | (base) [ehspector@milan2 de_novo]$ cd ../../
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd ../
| |
| − | (base) [ehspector@milan2 AMS_536]$ ls
| |
| − | class_project commands.txt Notes.txt Tutorials
| |
| − | (base) [ehspector@milan2 AMS_536]$ vi Notes.txt
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/1O86/de_novo/
| |
| − | (base) [ehspector@milan2 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2 Du.in
| |
| − | (base) [ehspector@milan2 de_novo]$ vi Du.in
| |
| − | (base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
| |
| − | /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
| |
| − | (base) [ehspector@milan2 de_novo]$ vi Du.in
| |
| − | (base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm_99
| |
| − | ls: cannot access '/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm_99': No such file or directory
| |
| − | (base) [ehspector@milan2 de_novo]$ ls /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw
| |
| − | ls: cannot access '/gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw': No such file or directory
| |
| − | (base) [ehspector@milan2 de_novo]$ cd /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/
| |
| − | (base) [ehspector@milan2 parameters]$ ls
| |
| − | 1 fraglib_linker.mol2 prot.table.ambcrg.sybH
| |
| − | antechamber fraglib_scaffold.mol2 sa_fraglib.dat
| |
| − | chem.defn fraglib_sidechain.mol2 screen.in
| |
| − | chemgrid fraglib_torenv.dat screen.para
| |
| − | chem_match.tbl leap vdw_AMBER_parm94.defn
| |
| − | flex.defn na.table.ambcrg vdw_AMBER_parm94.dock3_7.defn
| |
| − | flex_drive_mod.tbl pains_table_2019_09_01.dat vdw_AMBER_parm94.dock3_7_one_C_3.defn
| |
| − | flex_drive.tbl pains_table.dat vdw_AMBER_parm96.defn
| |
| − | flex_just_OH.defn ph4.defn vdw_AMBER_parm99.defn
| |
| − | flex_mod2.defn prot.table.ambcrg.ambH vdw_de_novo.defn
| |
| − | flex_mod.defn prot.table.ambcrg.pdb3H vdw.parms.amb
| |
| − | fraglib_ga_scaffold.mol2 prot.table.ambcrg.pdbH vdw.parms.update.amb
| |
| − | (base) [ehspector@milan2 parameters]$ class
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd ls
| |
| − | -bash: cd: ls: No such file or directory
| |
| − | (base) [ehspector@milan2 AMS_536]$ cd Tutorials/1O86/de_novo/
| |
| − | (base) [ehspector@milan2 de_novo]$ vi Du.in
| |
| − | (base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
| |
| − | (base) [ehspector@milan2 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2 Du.in Du.out
| |
| − | (base) [ehspector@milan2 de_novo]$ vi Du.out
| |
| − | (base) [ehspector@milan2 de_novo]$ cd ..
| |
| − | (base) [ehspector@milan2 1O86]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore de_novo
| |
| − | 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min commands.txt
| |
| − | (base) [ehspector@milan2 1O86]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 2w26/ga_calc/
| |
| − | (base) [ehspector@milan2 ga_calc]$ ;s
| |
| − | -bash: syntax error near unexpected token `;'
| |
| − | (base) [ehspector@milan2 ga_calc]$ ls
| |
| − | 2w26_fraglib.in 2w26_fraglib_scored.mol2 lib.sh
| |
| − | 2W26_fraglib_linker.mol2 2W26_fraglib_sidechain.mol2 py.sh
| |
| − | 2w26_fraglib.out 2W26_fraglib_torenv.dat unique_full_sorted_fraglib.dat
| |
| − | 2W26_fraglib_rigid.mol2 full_fraglib.dat
| |
| − | 2W26_fraglib_scaffold.mol2 full_sorted_fraglib.dat
| |
| − | (base) [ehspector@milan2 ga_calc]$ vi 2w26_fraglib.in
| |
| − | (base) [ehspector@milan2 ga_calc]$ cd ..
| |
| − | (base) [ehspector@milan2 2w26]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/
| |
| − | (base) [ehspector@milan2 1O86]$ mkdir ga_calc
| |
| − | (base) [ehspector@milan2 1O86]$ cd ..
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/2w26_fraglib.in 1O86/ga_calc/1O86_fraglib.in
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/lib.sh 1O86/ga_calc/lib.sh
| |
| − | (base) [ehspector@milan2 Tutorials]$ cp 2w26/ga_calc/py.sh 1O86/ga_calc/py.sh
| |
| − | (base) [ehspector@milan2 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan2 Tutorials]$ cd 1O86/
| |
| − | (base) [ehspector@milan2 1O86]$ ls
| |
| − | 001_structure 003_gridbox 005_dock 007_virtualscreen 009_rescore de_novo
| |
| − | 002_surface_spheres 004_energymin 006_footprint 008_cartesian_min commands.txt ga_calc
| |
| − | (base) [ehspector@milan2 1O86]$ cd ga_calc/
| |
| − | (base) [ehspector@milan2 ga_calc]$ ls
| |
| − | 1O86_fraglib.in lib.sh py.sh
| |
| − | (base) [ehspector@milan2 ga_calc]$ vi 1O86_fraglib.in
| |
| − | (base) [ehspector@milan2 ga_calc]$ vi lib.sh
| |
| − | (base) [ehspector@milan2 ga_calc]$ bash lib.sh
| |
| − | (base) [ehspector@milan2 ga_calc]$ ls
| |
| − | 1O86_fraglib.in 1O86_fraglib_rigid.mol2 1O86_fraglib_sidechain.mol2 py.sh
| |
| − | 1O86_fraglib_linker.mol2 1O86_fraglib_scaffold.mol2 1O86_fraglib_torenv.dat
| |
| − | 1O86_fraglib.out 1O86_fraglib_scored.mol2 lib.sh
| |
| − | (base) [ehspector@milan2 ga_calc]$ vi 1O86_fraglib.out
| |
| − | (base) [ehspector@milan2 ga_calc]$ ls
| |
| − | 1O86_fraglib.in 1O86_fraglib_rigid.mol2 1O86_fraglib_sidechain.mol2 py.sh
| |
| − | 1O86_fraglib_linker.mol2 1O86_fraglib_scaffold.mol2 1O86_fraglib_torenv.dat
| |
| − | 1O86_fraglib.out 1O86_fraglib_scored.mol2 lib.sh
| |
| − | (base) [ehspector@milan2 ga_calc]$ vi py.sh
| |
| − | (base) [ehspector@milan2 ga_calc]$ module list
| |
| − | Currently Loaded Modulefiles:
| |
| − | 1) slurm/seawulf3/21.08.8 3) gcc/13.2.0 5) gcc-stack
| |
| − | 2) shared 4) mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan2 ga_calc]$ module load python
| |
| − | (base) [ehspector@milan2 ga_calc]$ bash py.sh
| |
| − | (base) [ehspector@milan2 ga_calc]$ ls
| |
| − | 1O86_fraglib.in 1O86_fraglib_scored.mol2 lib.sh
| |
| − | 1O86_fraglib_linker.mol2 1O86_fraglib_sidechain.mol2 py.sh
| |
| − | 1O86_fraglib.out 1O86_fraglib_torenv.dat unique_full_sorted_fraglib.dat
| |
| − | 1O86_fraglib_rigid.mol2 full_fraglib.dat
| |
| − | 1O86_fraglib_scaffold.mol2 full_sorted_fraglib.dat
| |
| − | (base) [ehspector@milan2 ga_calc]$ pwd
| |
| − | /gpfs/home/ehspector/AMS_536/Tutorials/1O86/ga_calc
| |
| − | (base) [ehspector@milan2 ga_calc]$ cd ../de_novo/
| |
| − | (base) [ehspector@milan2 de_novo]$ vi Du.in
| |
| − | (base) [ehspector@milan2 de_novo]$ vi Du.in
| |
| − | (base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
| |
| − | (base) [ehspector@milan2 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2 Du.in Du.out
| |
| − | (base) [ehspector@milan2 de_novo]$ vi Du.out
| |
| − | (base) [ehspector@milan2 de_novo]$ vi Du.in
| |
| − | (base) [ehspector@milan2 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
| |
| − | Segmentation fault (core dumped)
| |
| − | (base) [ehspector@milan2 de_novo]$ la
| |
| − | -bash: la: command not found
| |
| − | (base) [ehspector@milan2 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2 Du.in Du.out Du.out.denovo_build.mol2
| |
| − | (base) [ehspector@milan2 de_novo]$ vi Du.out
| |
| − | (base) [ehspector@milan2 de_novo]$ vi 1O86_ligand_Du.mol2
| |
| − | (base) [ehspector@milan2 de_novo]$ exit
| |
| − | logout
| |
| − | Connection to milan.seawulf.stonybrook.edu closed.
| |
| − | (base) supremestudier@Evans-MBP Tutorial % ssh -X ehspector@milan.seawulf.stonybrook.edu
| |
| − | ehspector@milan.seawulf.stonybrook.edu's password:
| |
| − | Duo two-factor login for ehspector
| |
| − |
| |
| − | Enter a passcode or select one of the following options:
| |
| − |
| |
| − | 1. Duo Push to XXX-XXX-9204
| |
| − |
| |
| − | Passcode or option (1-1): 1
| |
| − |
| |
| − | Pushed a login request to your device...
| |
| − | Success. Logging you in...
| |
| − | Loading gcc-stack
| |
| − | Loading requirement: gcc/13.2.0 mvapich2/gcc13.2/2.3.7
| |
| − | (base) [ehspector@milan1 ~]$ class
| |
| − | (base) [ehspector@milan1 AMS_536]$ cd Tutorials/
| |
| − | (base) [ehspector@milan1 Tutorials]$ ls
| |
| − | 1O86 2w26 5EEN
| |
| − | (base) [ehspector@milan1 Tutorials]$ cd 1O86/de_novo/
| |
| − | (base) [ehspector@milan1 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2 Du.in Du.out Du.out.denovo_build.mol2
| |
| − | (base) [ehspector@milan1 de_novo]$ vi Du.out.denovo_build.mol2
| |
| − | (base) [ehspector@milan1 de_novo]$ vi Du.out
| |
| − | (base) [ehspector@milan1 de_novo]$ vi Du.in
| |
| − | (base) [ehspector@milan1 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2 Du.in Du.out Du.out.denovo_build.mol2
| |
| − | (base) [ehspector@milan1 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
| |
| − | Segmentation fault (core dumped)
| |
| − | (base) [ehspector@milan1 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2 Du.in Du.out Du.out.denovo_build.mol2
| |
| − | (base) [ehspector@milan1 de_novo]$ vi Du.out
| |
| − | (base) [ehspector@milan1 de_novo]$ vi Du.out.denovo_build.mol2
| |
| − | (base) [ehspector@milan1 de_novo]$ vi Du.out
| |
| − | (base) [ehspector@milan1 de_novo]$ vi 1O86_ligand_Du.mol2
| |
| − | (base) [ehspector@milan1 de_novo]$ rm 1O86_ligand_Du.mol2
| |
| − | (base) [ehspector@milan1 de_novo]$ ls
| |
| − | Du.in Du.out Du.out.denovo_build.mol2
| |
| − | (base) [ehspector@milan1 de_novo]$ rm Du.out
| |
| − | (base) [ehspector@milan1 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2 Du.in Du.out.denovo_build.mol2
| |
| − | (base) [ehspector@milan1 de_novo]$ /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/bin/dock6 -i Du.in -o Du.out
| |
| − | (base) [ehspector@milan1 de_novo]$ ls
| |
| − | 1O86_ligand_Du.mol2 Du.out Du.out.completed.denovo_build.mol2
| |
| − | Du.in Du.out.anchor_1.root_layer_1.mol2 Du.out.denovo_build.mol2
| |
| − | (base) [ehspector@milan1 de_novo]$ vi Du.out
| |
| − | (base) [ehspector@milan1 de_novo]$ vi Du.in
| |
| − |
| |
| − | conformer_search_type denovo
| |
| − | dn_fraglib_scaffold_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_scaffold.mol2
| |
| − | dn_fraglib_linker_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_linker.mol2
| |
| − | dn_fraglib_sidechain_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/fraglib_sidechain.mol2
| |
| − | dn_user_specified_anchor yes
| |
| − | dn_fraglib_anchor_file 1O86_ligand_Du.mol2
| |
| − | dn_torenv_table ../ga_calc/unique_full_sorted_fraglib.dat
| |
| − | dn_name_identifier denovo
| |
| − | dn_sampling_method graph
| |
| − | dn_graph_max_picks 30
| |
| − | dn_graph_breadth 3
| |
| − | dn_graph_depth 2
| |
| − | dn_graph_temperature 100.0
| |
| − | dn_pruning_conformer_score_cutoff 100.0
| |
| − | dn_pruning_conformer_score_scaling_factor 2.0
| |
| − | dn_pruning_clustering_cutoff 100.0
| |
| − | dn_remove_duplicates yes
| |
| − | dn_max_duplicates_per_mol 0
| |
| − | dn_write_pruned_duplicates no
| |
| − | dn_advanced_pruning yes
| |
| − | dn_prune_initial_sample yes
| |
| − | dn_sample_torsions yes
| |
| − | dn_prune_individual_torsions yes
| |
| − | dn_prune_combined_torsions yes
| |
| − | dn_random_root_selection no
| |
| − | dn_mol_wt_cutoff_type soft
| |
| − | dn_upper_constraint_mol_wt 1000
| |
| − | dn_lower_constraint_mol_wt 0.0
| |
| − | dn_mol_wt_std_dev 35.0
| |
| − | dn_constraint_rot_bon 15
| |
| − | dn_constraint_formal_charge 2.0
| |
| − | dn_heur_unmatched_num 1
| |
| − | dn_heur_matched_rmsd 2.0
| |
| − | dn_unique_anchors 1
| |
| − | dn_max_grow_layers 1
| |
| − | dn_max_root_size 25
| |
| − | dn_max_layer_size 25
| |
| − | dn_max_current_aps 5
| |
| − | dn_max_scaffolds_per_layer 1
| |
| − | dn_max_successful_att_per_root 50000
| |
| − | dn_write_checkpoints yes
| |
| − | dn_write_prune_dump yes
| |
| − | dn_write_orients no
| |
| − | dn_write_growth_trees no
| |
| − | dn_output_prefix Du.out
| |
| − | use_internal_energy yes
| |
| − | internal_energy_rep_exp 12
| |
| − | internal_energy_cutoff 100.0
| |
| − | use_database_filter no
| |
| − | orient_ligand no
| |
| − | bump_filter no
| |
| − | score_molecules yes
| |
| − | contact_score_primary no
| |
| − | grid_score_primary yes
| |
| − | grid_score_rep_rad_scale 1
| |
| − | grid_score_vdw_scale 1
| |
| − | grid_score_es_scale 1
| |
| − | grid_lig_efficiency no
| |
| − | grid_score_grid_prefix ../003_gridbox/grid
| |
| − | minimize_ligand yes
| |
| − | minimize_anchor yes
| |
| − | minimize_flexible_growth yes
| |
| − | use_advanced_simplex_parameters no
| |
| − | simplex_max_cycles 1
| |
| − | simplex_score_converge 0.1
| |
| − | simplex_cycle_converge 1.0
| |
| − | simplex_trans_step 1.0
| |
| − | simplex_rot_step 0.1
| |
| − | simplex_tors_step 10.0
| |
| − | simplex_anchor_max_iterations 500
| |
| − | simplex_grow_max_iterations 500
| |
| − | simplex_grow_tors_premin_iterations 0
| |
| − | simplex_final_min no
| |
| − | simplex_random_seed 0
| |
| − | simplex_restraint_min no
| |
| − | atom_model all
| |
| − | vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/vdw_AMBER_parm99.defn
| |
| − | flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex.defn
| |
| − | flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.12_ams536/parameters/flex_drive.tbl
| |
UCSF Chimera is a python-based, open-source molecular visualization and manipulation software suite. It is extremely helpful for both preparing molecules/receptors for docking and for visually analyzing the results of those calculations.
Once Chimera has installed, you can open it to find a blank blue-ish window, with a row of tabs along the top. Throughout this tutorial, you will be instructed to perform different actions contained within these tabs. We will denote the specific tab and sub-tab to be accessed by >> signs. For example, File >> Open PDB would indicate that you should click on the File tab, then mouse to and click Open PDB. This is necessary because some actions are nested in multiple sub-tabs (for instance, selecting all hydrogens in a model would require Select >> Chemistry >> element >> H, as shown below)
More extensive documentation on Chimera and its functions is available on the official site.
Having setup your necessary environment to work on seawulf, lets navigate to your local computer and begin
the protein preparation process:
To begin protein preparation you will need the necessary PDB file to work with. Using this link: https://www.rcsb.org/structure/1O86,
you will see the RCSB main page opened to our protein of choice:
Next, you'll want to navigate to the top right corner where it says Download Files. Then, select the dropdown arrow.
The following pulldown menu will appear on the screen:
Now that you have the PDB file, lets navigate to Chimera program to open the file.
1. Open 1O86 protein only file in chimera and hit select > show> surface
2. Write the DMS file by choosing tools>structure editing>Write DMS
3. Upload the DMS file to your directory
4. Create a sphere input file using the following command:
5. Paste the following into your input file:
6. Run the program with the following command
Based on the overlay the ribbons are aligned with the spheres indicating the generation of surface spheres was successful.
Slurm and queue etiquette, VS .in explanation and queue submission, ViewDock in Chimera
Explanation of rationale for GA and basic functionality, sample input file and expected outputs
Explanation of rationale for DN and basic functionality, sample input file and expected outputs
To prepare our molecule for a De Novo calculation, we must first select a dummy atom to 'grow'
from. To do this, first open your 1O86_fixed_protein_H_cH.mol2 file, then your 1O86_ligand_H_cH.mol2.
The rationale for this is we would like to delete an atom on the ligand that contains a group
that interacts with the protein. This will help to produce meaningful results, from a drug design standpoint:
As you can see it is a little difficult to see which atoms are interacting with the protein.
To refine this inspection, hit Control and select an atom on the ligand.
Then, hit the up arrow to highlight the entire ligand.
Next, hit Select --> Zone and the following menu appears:
Lets modify the Zone and change the number from 5.0 angstroms to 3.0 angstroms.
Additionally, make sure that that the third box is checked off entitled that selects neighboring residues.
Then, press okay. You will notice that your ligand and the neighboring residues are highlighted:
To modify this image even further:
Go to Actions --> Atoms/Bonds --> hit Show
Next, navigate to Select --> press Invert(selected models), here you'll notice most of the protein is highlighted
Lastly, Return to Actions --> Atoms/Bonds --> hit delete
You now see that there is a clearer picture of specifically, which atoms are interacting closely with the protein
You'll notice that there are two oxygens interacting with neighboring residues in the protein. Tracing your cursor
in between the oxygens, you'll highlight a Carbon atom labeled C9. This will be the atom of choice for this tutorial.
Now that we have our atom of choice, we need to modify the ligand as well as the mol2 file itself.
Locate the C9 atom --> select the two oxygens attached to C9 --> Atoms/Bonds --> delete.
Then, save the mol2 file, lets call it 1O86_ligand_Du.mol2.
Finally, we must open the mol2 file on our terminal and change the atom type of C9 to Du:
Find the C9 atom and modify the atom type. Your input file should look like this:
Save it.
